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HEADER HYDROLASE 28-JUN-99 1QTR
TITLE CRYSTAL STRUCTURE ANALYSIS OF THE PROLYL AMINOPEPTIDASE
TITLE 2 FROM SERRATIA MARCESCENS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROLYL AMINOPEPTIDASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.4.11.5;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 EXPRESSION_SYSTEM: SERRATIA MARCESCENS;
SOURCE 3 EXPRESSION_SYSTEM_COMMON: BACTERIA
KEYWDS ALPHA BETA HYDROLASE FOLD, PROLINE, PROLYL AMINOPEPTIDASE,
KEYWDS 2 SERRATIA, IMINOPEPTIDASE
EXPDTA X-RAY DIFFRACTION
AUTHOR T.YOSHIMOTO,T.KABASHIMA,K.UCHIKAWA,T.INOUE,N.TANAKA
REVDAT 2 29-DEC-99 1QTR 1 JRNL CRYST1
REVDAT 1 07-JUL-99 1QTR 0
JRNL AUTH T.YOSHIMOTO,T.KABASHIMA,K.UCHIKAWA,T.INOUE,
JRNL AUTH 2 N.TANAKA,K.T.NAKAMURA,M.TSURU,K.ITO
JRNL TITL CRYSTAL STRUCTURE OF THE PROLYL AMINOPEPTIDASE
JRNL TITL 2 FROM SERRATIA MARCESCENS
JRNL REF J.BIOCHEM.(TOKYO) V. 126 559 1999
JRNL REFN ASTM JOBIAO JA ISSN 0021-924X
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH T.KABASHIMA,A.KITAZONO,A.KITANO,K.INOUE,T.YOSHIMOTO
REMARK 1 TITL PROLYL AMINOPEPTIDASE FROM SERRATIA MARCESCENS :
REMARK 1 TITL 2 SEQUENCING AND EXPRESSION
REMARK 1 REF J.BIOCHEM.(TOKYO) V. 122 601 1997
REMARK 1 REFN ASTM JOBIAO JA ISSN 0021-924X
REMARK 1 REFERENCE 2
REMARK 1 AUTH A.KITAZONO,K.ITO,T.YOSHIMOTO
REMARK 1 TITL PROLYL AMINOPEPTIDASE IS NOT A SULFHYDRYL ENZYME:
REMARK 1 TITL 2 IDENTIFICATION OF THE ACTIVE SERINE RESIDUE BY
REMARK 1 TITL 3 SITE-DIRECTED MUTAGENESIS
REMARK 1 REF J.BIOCHEM.(TOKYO) V. 116 943 1994
REMARK 1 REFN ASTM JOBIAO JA ISSN 0021-924X
REMARK 2
REMARK 2 RESOLUTION. 2.32 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.32
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000
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 : 45646
REMARK 3
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) : 0.189
REMARK 3 FREE R VALUE : 0.267
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
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 : 2530
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
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 1QTR COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-1999.
REMARK 100 THE RCSB ID CODE IS RCSB009256.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 25-OCT-1997
REMARK 200 TEMPERATURE (KELVIN) : 293.0
REMARK 200 PH : 6.50
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS
REMARK 200 DATA SCALING SOFTWARE : R-AXIS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45646
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.320
REMARK 200 RESOLUTION RANGE LOW (A) : 10.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 89.1
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.05900
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) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
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: NULL
REMARK 200 SOFTWARE USED: DM
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): NULL
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG6000, SODIUM ACETATE, NA
REMARK 280 CACODYLATE/KH2PO4
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,1/2+Z
REMARK 290 3555 1/2-Y,1/2+X,3/4+Z
REMARK 290 4555 1/2+Y,1/2-X,1/4+Z
REMARK 290 5555 1/2-X,1/2+Y,3/4-Z
REMARK 290 6555 1/2+X,1/2-Y,1/4-Z
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,1/2-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 84.60000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.68000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.68000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 126.90000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.68000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.68000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.30000
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.68000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.68000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 126.90000
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.68000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.68000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 42.30000
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 84.60000
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 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 GLY A 46 N - CA - C ANGL. DEV. =-10.6 DEGREES
REMARK 500 LYS A 65 N - CA - C ANGL. DEV. =-11.9 DEGREES
REMARK 500 GLN A 71 N - CA - C ANGL. DEV. = 16.5 DEGREES
REMARK 500 ARG A 78 N - CA - C ANGL. DEV. = 14.4 DEGREES
REMARK 500 ASP A 84 N - CA - C ANGL. DEV. =-10.6 DEGREES
REMARK 500 LEU A 242 CA - CB - CG ANGL. DEV. = 12.2 DEGREES
REMARK 500 GLU A 300 N - CA - C ANGL. DEV. =-10.5 DEGREES
DBREF 1QTR A 4 317 GB BAA23336 G2605615 4 317
SEQRES 1 A 314 LEU ARG GLY LEU TYR PRO PRO LEU ALA ALA TYR ASP SER
SEQRES 2 A 314 GLY TRP LEU ASP THR GLY ASP GLY HIS ARG ILE TYR TRP
SEQRES 3 A 314 GLU LEU SER GLY ASN PRO ASN GLY LYS PRO ALA VAL PHE
SEQRES 4 A 314 ILE HIS GLY GLY PRO GLY GLY GLY ILE SER PRO HIS HIS
SEQRES 5 A 314 ARG GLN LEU PHE ASP PRO GLU ARG TYR LYS VAL LEU LEU
SEQRES 6 A 314 PHE ASP GLN ARG GLY CYS GLY ARG SER ARG PRO HIS ALA
SEQRES 7 A 314 SER LEU ASP ASN ASN THR THR TRP HIS LEU VAL ALA ASP
SEQRES 8 A 314 ILE GLU ARG LEU ARG GLU MET ALA GLY VAL GLU GLN TRP
SEQRES 9 A 314 LEU VAL PHE GLY GLY SER TRP GLY SER THR LEU ALA LEU
SEQRES 10 A 314 ALA TYR ALA GLN THR HIS PRO GLU ARG VAL SER GLU MET
SEQRES 11 A 314 VAL LEU ARG GLY ILE PHE THR LEU ARG LYS GLN ARG LEU
SEQRES 12 A 314 HIS TRP TYR TYR GLN ASP GLY ALA SER ARG PHE PHE PRO
SEQRES 13 A 314 GLU LYS TRP GLU ARG VAL LEU SER ILE LEU SER ASP ASP
SEQRES 14 A 314 GLU ARG LYS ASP VAL ILE ALA ALA TYR ARG GLN ARG LEU
SEQRES 15 A 314 THR SER ALA ASP PRO GLN VAL GLN LEU GLU ALA ALA LYS
SEQRES 16 A 314 LEU TRP SER VAL TRP GLU GLY GLU THR VAL THR LEU LEU
SEQRES 17 A 314 PRO SER ARG GLU SER ALA SER PHE GLY GLU ASP ASP PHE
SEQRES 18 A 314 ALA LEU ALA PHE ALA ARG ILE GLU ASN HIS TYR PHE THR
SEQRES 19 A 314 HIS LEU GLY PHE LEU GLU SER ASP ASP GLN LEU LEU ARG
SEQRES 20 A 314 ASN VAL PRO LEU ILE ARG HIS ILE PRO ALA VAL ILE VAL
SEQRES 21 A 314 HIS GLY ARG TYR ASP MET ALA CYS GLN VAL GLN ASN ALA
SEQRES 22 A 314 TRP ASP LEU ALA LYS ALA TRP PRO GLU ALA GLU LEU HIS
SEQRES 23 A 314 ILE VAL GLU GLY ALA GLY HIS SER TYR ASP GLU PRO GLY
SEQRES 24 A 314 ILE LEU HIS GLN LEU MET ILE ALA THR ASP ARG PHE ALA
SEQRES 25 A 314 GLY LYS
HELIX 1 1 SER A 52 GLN A 57 5 6
HELIX 2 2 THR A 87 GLY A 103 1 17
HELIX 3 3 SER A 113 GLN A 124 1 12
HELIX 4 4 ARG A 142 GLN A 151 1 10
HELIX 5 5 ALA A 154 PHE A 157 5 4
HELIX 6 6 PHE A 158 ILE A 168 1 11
HELIX 7 7 ASP A 171 LYS A 175 5 5
HELIX 8 8 ASP A 176 THR A 186 1 11
HELIX 9 9 ASP A 189 VAL A 208 1 20
HELIX 10 10 SER A 213 GLY A 220 5 8
HELIX 11 11 GLU A 221 HIS A 238 1 18
HELIX 12 12 LEU A 239 LEU A 242 5 4
HELIX 13 13 ASN A 251 ARG A 256 5 6
HELIX 14 14 GLN A 272 TRP A 283 1 12
HELIX 15 15 GLU A 300 GLY A 316 1 17
SHEET 1 A 8 ASP A 15 ASP A 20 0
SHEET 2 A 8 ARG A 26 GLY A 33 -1 N ILE A 27 O LEU A 19
SHEET 3 A 8 TYR A 64 PHE A 69 -1 N VAL A 66 O SER A 32
SHEET 4 A 8 LYS A 38 ILE A 43 1 O LYS A 38 N LYS A 65
SHEET 5 A 8 TRP A 107 GLY A 112 1 O LEU A 108 N VAL A 41
SHEET 6 A 8 VAL A 130 ARG A 136 1 N SER A 131 O TRP A 107
SHEET 7 A 8 ALA A 260 GLY A 265 1 O VAL A 261 N LEU A 135
SHEET 8 A 8 GLU A 287 VAL A 291 1 O GLU A 287 N ILE A 262
CRYST1 65.360 65.360 169.200 90.00 90.00 90.00 P 43 21 2 8
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 0.015300 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015300 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005910 0.00000
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