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HEADER HYDROLASE 12-MAY-06 2GZS
TITLE ENTEROBACTIN HYDOLASE IROE COMPLEX WITH DFP
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 ENTEROBACTIN, SALMOCHELIN, DFP, HYDROLASE, CATALYTIC DYAD
EXPDTA X-RAY DIFFRACTION
AUTHOR N.A.LARSEN,C.T.WALSH
REVDAT 1 05-SEP-06 2GZS 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. 1.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SHELXL-97
REMARK 3 AUTHORS : G.M.SHELDRICK
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : NULL
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.174
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : 0.186
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3961
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 80830
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.163
REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 65525
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1954
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 10
REMARK 3 SOLVENT ATOMS : 197
REMARK 3
REMARK 3 MODEL REFINEMENT.
REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2162.00
REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00
REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0
REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 8651
REMARK 3 NUMBER OF RESTRAINTS : 8093
REMARK 3
REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK 3 BOND LENGTHS (A) : 0.016
REMARK 3 ANGLE DISTANCES (A) : 0.035
REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000
REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.029
REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.073
REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.099
REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.024
REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000
REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.078
REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED: NULL
REMARK 3
REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER
REMARK 3 SPECIAL CASE: NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2GZS COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006
REMARK 4
REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY.
REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-18)
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB .
REMARK 100 THE RCSB ID CODE IS RCSB037750.
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, 0.9798, 0.9184
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 : 79213
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400
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 (%) : 93.7
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) : 1.40
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45
REMARK 200 COMPLETENESS FOR SHELL (%) : 84.6
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: MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: SOLVE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 31.92
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 5-10% PEG 3350, 100 MM HEPES, 500
REMARK 280 MM DFP, PH 7.5, VAPOR DIFFUSION, HANGING 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 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: 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 -119.27 67.12
REMARK 500 SER A 245 -90.39 50.40
REMARK 525
REMARK 525 SOLVENT
REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED
REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE
REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL
REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH 1193 DISTANCE = 5.26 ANGSTROMS
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2GZR RELATED DB: PDB
DBREF 2GZS A 41 318 UNP Q6KD95 Q6KD95_ECOLI 41 318
SEQADV 2GZS MSE A 88 UNP Q6KD95 MET 88 MODIFIED RESIDUE
SEQADV 2GZS MSE A 95 UNP Q6KD95 MET 95 MODIFIED RESIDUE
SEQADV 2GZS MSE A 242 UNP Q6KD95 MET 242 MODIFIED RESIDUE
SEQADV 2GZS MSE A 290 UNP 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 2GZS MSE A 88 MET SELENOMETHIONINE
MODRES 2GZS MSE A 95 MET SELENOMETHIONINE
MODRES 2GZS MSE A 242 MET SELENOMETHIONINE
MODRES 2GZS 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
HET DFP A1189 10
HETNAM MSE SELENOMETHIONINE
HETNAM DFP DIISOPROPYL PHOSPHONATE
FORMUL 1 MSE 4(C5 H11 N O2 SE)
FORMUL 2 DFP C6 H15 O3 P
FORMUL 3 HOH *197(H2 O)
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 SER A 107 1 9
HELIX 4 4 ASP A 126 TYR A 134 1 9
HELIX 5 5 PRO A 136 ARG A 141 5 6
HELIX 6 6 GLY A 156 ARG A 167 1 12
HELIX 7 7 ARG A 167 GLU A 173 1 7
HELIX 8 8 SER A 189 SER A 202 1 14
HELIX 9 9 PRO A 213 GLY A 216 5 4
HELIX 10 10 GLY A 218 ALA A 228 1 11
HELIX 11 11 GLY A 258 LYS A 273 1 16
HELIX 12 12 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 VAL A 69 N THR A 56
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 117
SHEET 5 A 8 ILE A 178 HIS A 188 1 O GLY A 184 N ILE A 85
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 ALA A 240 N TYR A 208
SHEET 8 A 8 ALA A 277 ASP A 281 1 O TRP A 280 N ILE A 241
LINK OG SER A 189 P DFP A1189
CRYST1 36.295 38.361 44.631 113.10 93.99 98.08 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 0.027552 0.003911 0.003848 0.00000
SCALE2 0.000000 0.026330 0.011736 0.00000
SCALE3 0.000000 0.000000 0.024591 0.00000
TER 1955 GLU A 305
MASTER 228 0 5 12 8 0 0 6 2161 1 43 22
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