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HEADER HYDROLASE 11-MAY-06 2GZR
TITLE ENTEROBACTIN AND SALMOCHELIN HYDROLASE IROE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: IROE PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_COMMON: BACTERIA;
SOURCE 4 GENE: IROE;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA
KEYWDS SERINE HYDROLASE, CATALYTIC DYAD, ENTEROBACTIN
EXPDTA X-RAY DIFFRACTION
AUTHOR N.A.LARSEN,C.T.WALSH
REVDAT 1 05-SEP-06 2GZR 0
JRNL AUTH N.A.LARSEN,H.LIN,R.WEI,M.A.FISCHBACH,C.T.WALSH
JRNL TITL STRUCTURAL CHARACTERIZATION OF ENTEROBACTIN
JRNL TITL 2 HYDROLASE IROE.
JRNL REF BIOCHEMISTRY V. 45 10184 2006
JRNL REFN ASTM BICHAW US ISSN 0006-2960
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 16903
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.203
REMARK 3 FREE R VALUE : 0.268
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 815
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1895
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : NULL
REMARK 3 BOND ANGLES (DEGREES) : NULL
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2GZR COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-2006.
REMARK 100 THE RCSB ID CODE IS RCSB037749.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-FEB-2006
REMARK 200 TEMPERATURE (KELVIN) : 120.0
REMARK 200 PH : 7.50
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ALS
REMARK 200 BEAMLINE : 8.2.1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97960
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18258
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35
REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 2GZS
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 28.66
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 6-10% PEG 3350, 100 MM HEPES, PH
REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR
REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 SER A 140
REMARK 465 ARG A 141
REMARK 465 LYS A 142
REMARK 465 THR A 143
REMARK 465 ASP A 144
REMARK 465 LEU A 145
REMARK 465 HIS A 146
REMARK 465 SER A 147
REMARK 465 GLY A 148
REMARK 465 ARG A 149
REMARK 465 PHE A 150
REMARK 465 SER A 151
REMARK 465 THR A 247
REMARK 465 GLN A 248
REMARK 465 GLY A 249
REMARK 465 ASP A 250
REMARK 465 ASN A 251
REMARK 465 ARG A 252
REMARK 465 GLU A 253
REMARK 465 THR A 254
REMARK 465 HIS A 255
REMARK 465 ALA A 256
REMARK 465 VAL A 257
REMARK 465 ASN A 306
REMARK 465 ALA A 307
REMARK 465 ASN A 308
REMARK 465 TYR A 309
REMARK 465 THR A 310
REMARK 465 ALA A 311
REMARK 465 GLY A 312
REMARK 465 CYS A 313
REMARK 465 HIS A 314
REMARK 465 GLU A 315
REMARK 465 LEU A 316
REMARK 465 SER A 317
REMARK 465 HIS A 318
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 PRO A 41 CB PRO A 41 CG 0.053
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 PRO A 84 N - CA - C ANGL. DEV. = -9.0 DEGREES
REMARK 500 VAL A 113 N - CA - C ANGL. DEV. =-10.1 DEGREES
REMARK 500 ASP A 179 N - CA - C ANGL. DEV. =-10.5 DEGREES
REMARK 500 SER A 201 N - CA - C ANGL. DEV. = 8.0 DEGREES
REMARK 500 SER A 203 N - CA - C ANGL. DEV. = -8.2 DEGREES
REMARK 500 ASN A 284 N - CA - C ANGL. DEV. = 8.1 DEGREES
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 SER A 189 -114.20 63.65
REMARK 500 SER A 245 -49.56 63.00
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2GZS RELATED DB: PDB
DBREF 2GZR A 41 318 UNP Q6KD95 Q6KD95_ECOLI 41 318
SEQADV 2GZR MSE A 88 GB Q6KD95 MET 88 MODIFIED RESIDUE
SEQADV 2GZR MSE A 95 GB Q6KD95 MET 95 MODIFIED RESIDUE
SEQADV 2GZR MSE A 242 GB Q6KD95 MET 242 MODIFIED RESIDUE
SEQADV 2GZR MSE A 290 GB Q6KD95 MET 290 MODIFIED RESIDUE
SEQRES 1 A 278 PRO ASN ILE ALA ASP LYS GLY SER VAL PHE TYR HIS PHE
SEQRES 2 A 278 SER ALA THR SER PHE ASP SER VAL ASP GLY THR ARG HIS
SEQRES 3 A 278 TYR ARG VAL TRP THR ALA VAL PRO ASN THR THR ALA PRO
SEQRES 4 A 278 ALA SER GLY TYR PRO ILE LEU TYR MSE LEU ASP GLY ASN
SEQRES 5 A 278 ALA VAL MSE ASP ARG LEU ASP ASP GLU LEU LEU LYS GLN
SEQRES 6 A 278 LEU SER GLU LYS THR PRO PRO VAL ILE VAL ALA VAL GLY
SEQRES 7 A 278 TYR GLN THR ASN LEU PRO PHE ASP LEU ASN SER ARG ALA
SEQRES 8 A 278 TYR ASP TYR THR PRO ALA ALA GLU SER ARG LYS THR ASP
SEQRES 9 A 278 LEU HIS SER GLY ARG PHE SER ARG LYS SER GLY GLY SER
SEQRES 10 A 278 ASN ASN PHE ARG GLN LEU LEU GLU THR ARG ILE ALA PRO
SEQRES 11 A 278 LYS VAL GLU GLN GLY LEU ASN ILE ASP ARG GLN ARG ARG
SEQRES 12 A 278 GLY LEU TRP GLY HIS SER TYR GLY GLY LEU PHE VAL LEU
SEQRES 13 A 278 ASP SER TRP LEU SER SER SER TYR PHE ARG SER TYR TYR
SEQRES 14 A 278 SER ALA SER PRO SER LEU GLY ARG GLY TYR ASP ALA LEU
SEQRES 15 A 278 LEU SER ARG VAL THR ALA VAL GLU PRO LEU GLN PHE CYS
SEQRES 16 A 278 THR LYS HIS LEU ALA ILE MSE GLU GLY SER ALA THR GLN
SEQRES 17 A 278 GLY ASP ASN ARG GLU THR HIS ALA VAL GLY VAL LEU SER
SEQRES 18 A 278 LYS ILE HIS THR THR LEU THR ILE LEU LYS ASP LYS GLY
SEQRES 19 A 278 VAL ASN ALA VAL PHE TRP ASP PHE PRO ASN LEU GLY HIS
SEQRES 20 A 278 GLY PRO MSE PHE ASN ALA SER PHE ARG GLN ALA LEU LEU
SEQRES 21 A 278 ASP ILE SER GLY GLU ASN ALA ASN TYR THR ALA GLY CYS
SEQRES 22 A 278 HIS GLU LEU SER HIS
MODRES 2GZR MSE A 88 MET SELENOMETHIONINE
MODRES 2GZR MSE A 95 MET SELENOMETHIONINE
MODRES 2GZR MSE A 242 MET SELENOMETHIONINE
MODRES 2GZR MSE A 290 MET SELENOMETHIONINE
HET MSE A 88 8
HET MSE A 95 8
HET MSE A 242 8
HET MSE A 290 8
HETNAM MSE SELENOMETHIONINE
FORMUL 1 MSE 4(C5 H11 N1 O2 SE1)
HELIX 1 1 PRO A 41 GLY A 47 1 7
HELIX 2 2 ASP A 90 LEU A 98 1 9
HELIX 3 3 ASP A 99 GLU A 108 1 10
HELIX 4 4 ASP A 126 TYR A 134 1 9
HELIX 5 5 GLY A 156 ARG A 167 1 12
HELIX 6 6 ARG A 167 GLU A 173 1 7
HELIX 7 7 SER A 189 SER A 202 1 14
HELIX 8 8 TYR A 219 ALA A 228 1 10
HELIX 9 9 PRO A 231 CYS A 235 5 5
HELIX 10 10 GLY A 258 LYS A 273 1 16
HELIX 11 11 GLY A 286 SER A 303 1 18
SHEET 1 A 8 TYR A 51 ASP A 59 0
SHEET 2 A 8 HIS A 66 PRO A 74 -1 O TYR A 67 N PHE A 58
SHEET 3 A 8 VAL A 113 TYR A 119 -1 O ILE A 114 N ALA A 72
SHEET 4 A 8 TYR A 83 MSE A 88 1 N MSE A 88 O VAL A 115
SHEET 5 A 8 ILE A 178 HIS A 188 1 O GLY A 184 N TYR A 87
SHEET 6 A 8 SER A 207 ALA A 211 1 O TYR A 209 N LEU A 185
SHEET 7 A 8 HIS A 238 GLU A 243 1 O MSE A 242 N SER A 210
SHEET 8 A 8 ASN A 276 ASP A 281 1 O VAL A 278 N LEU A 239
CRYST1 36.220 36.980 44.208 111.47 89.69 102.99 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.027609 0.006369 0.002411 0.00000
SCALE2 0.000000 0.027752 0.011204 0.00000
SCALE3 0.000000 0.000000 0.024395 0.00000
TER 1896 GLU A 305
MASTER 292 0 4 11 8 0 0 6 1895 1 32 22
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