HEADER HYDROLASE 07-JUN-07 2Z3W TITLE PROLYL TRIPEPTIDYL AMINOPEPTIDASE MUTANT E636A COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPEPTIDYL AMINOPEPTIDASE IV; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 39-732; COMPND 5 SYNONYM: PROLYL TRIPEPTIDYL AMINOPEPTIDASE; COMPND 6 EC: 3.4.14.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYROMONAS GINGIVALIS; SOURCE 3 ORGANISM_TAXID: 242619; SOURCE 4 STRAIN: W83; SOURCE 5 GENE: PG1361; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS PROLYL OLIGOPEPTIDASE FAMILY, PEPTIDASE FAMILY S9, SERINE PROTEASE, KEYWDS 2 PROLINE-SPECIFIC PEPTIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.XU,Y.NAKAJIMA,K.ITO,T.YOSHIMOTO REVDAT 5 01-NOV-23 2Z3W 1 REMARK REVDAT 4 10-NOV-21 2Z3W 1 REMARK SEQADV REVDAT 3 13-JUL-11 2Z3W 1 VERSN REVDAT 2 24-FEB-09 2Z3W 1 VERSN REVDAT 1 19-FEB-08 2Z3W 0 JRNL AUTH Y.XU,Y.NAKAJIMA,K.ITO,H.ZHENG,H.OYAMA,U.HEISER,T.HOFFMANN, JRNL AUTH 2 U.T.GARTNER,H.U.DEMUTH,T.YOSHIMOTO JRNL TITL NOVEL INHIBITOR FOR PROLYL TRIPEPTIDYL AMINOPEPTIDASE FROM JRNL TITL 2 PORPHYROMONAS GINGIVALIS AND DETAILS OF JRNL TITL 3 SUBSTRATE-RECOGNITION MECHANISM JRNL REF J.MOL.BIOL. V. 375 708 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18042490 JRNL DOI 10.1016/J.JMB.2007.09.077 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 66242 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3533 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4827 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 263 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5193 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 547 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.59000 REMARK 3 B22 (A**2) : -0.59000 REMARK 3 B33 (A**2) : 0.88000 REMARK 3 B12 (A**2) : -0.29000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.139 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.074 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5345 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7262 ; 1.449 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 650 ; 6.442 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 251 ;33.639 ;23.147 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 836 ;14.575 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;16.622 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 777 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4134 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2383 ; 0.199 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3594 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 554 ; 0.140 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 51 ; 0.156 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.159 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3333 ; 0.989 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5228 ; 1.561 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2332 ; 2.402 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2034 ; 3.628 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2Z3W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000027488. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 MONOCHROMETER REMARK 200 OPTICS : MONOCHROMETOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71953 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 81.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 19.10 REMARK 200 R MERGE FOR SHELL (I) : 0.31400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 11.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2D5L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.1M POTASSIUM SODIUM TARTRATE, 0.2M REMARK 280 LITHIUM SULFATE, 0.1M CHES BUFFER, PH 9.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 80.47150 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 80.47150 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 80.47150 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 80.47150 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 80.47150 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 80.47150 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 51940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 160.94300 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 MET A 27 REMARK 465 ARG A 28 REMARK 465 GLY A 29 REMARK 465 SER A 30 REMARK 465 HIS A 31 REMARK 465 HIS A 32 REMARK 465 HIS A 33 REMARK 465 HIS A 34 REMARK 465 HIS A 35 REMARK 465 HIS A 36 REMARK 465 GLY A 37 REMARK 465 SER A 38 REMARK 465 LEU A 39 REMARK 465 MET A 40 REMARK 465 PRO A 41 REMARK 465 GLY A 42 REMARK 465 GLY A 43 REMARK 465 LYS A 44 REMARK 465 GLU A 45 REMARK 465 PHE A 46 REMARK 465 TYR A 47 REMARK 465 ASN A 48 REMARK 465 PHE A 49 REMARK 465 TYR A 50 REMARK 465 PRO A 51 REMARK 465 GLU A 52 REMARK 465 ALA A 77 REMARK 465 ASN A 78 REMARK 465 GLY A 79 REMARK 465 LYS A 80 REMARK 465 SER A 81 REMARK 465 ALA A 82 REMARK 465 GLN A 83 REMARK 465 GLY A 99 REMARK 465 CYS A 100 REMARK 465 LYS A 101 REMARK 465 PHE A 102 REMARK 465 GLN A 103 REMARK 465 THR A 104 REMARK 465 THR A 105 REMARK 465 ASP A 106 REMARK 465 ALA A 107 REMARK 465 ASN A 471 REMARK 465 PRO A 472 REMARK 465 ASP A 473 REMARK 465 THR A 474 REMARK 465 GLY A 475 REMARK 465 TYR A 476 REMARK 465 SER A 532 REMARK 465 SER A 533 REMARK 465 VAL A 534 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TYR A 53 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 GLU A 98 CG CD OE1 OE2 REMARK 470 GLN A 126 CG CD OE1 NE2 REMARK 470 LYS A 470 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 922 O HOH A 1035 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 371 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 140 -70.84 -93.42 REMARK 500 HIS A 167 -13.30 84.86 REMARK 500 LEU A 177 115.64 -34.48 REMARK 500 SER A 404 142.01 179.64 REMARK 500 ARG A 452 126.66 -170.66 REMARK 500 ILE A 459 95.90 -51.86 REMARK 500 TYR A 518 -78.04 -121.02 REMARK 500 HIS A 522 -12.05 76.49 REMARK 500 ARG A 570 41.30 -142.78 REMARK 500 SER A 603 -119.57 72.67 REMARK 500 ASP A 645 -178.04 61.50 REMARK 500 ASN A 650 54.97 -143.48 REMARK 500 GLU A 709 -134.67 -88.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D5L RELATED DB: PDB REMARK 900 THE WILD-TYPE PROTEIN REMARK 900 RELATED ID: 2DCM RELATED DB: PDB REMARK 900 THE S603A MUTANT PROTEIN COMPLEXED WITH SUBSTRATE REMARK 900 RELATED ID: 2EEP RELATED DB: PDB REMARK 900 THE WILD-TYPE PROTEIN COMPLEXD WITH INHIBITOR REMARK 900 RELATED ID: 2Z3Z RELATED DB: PDB REMARK 900 THE SAME MUTANT ENZYME COMPLEXD WITH AN INHIBITOR DBREF 2Z3W A 39 732 UNP Q7MUW6 Q7MUW6_PORGI 39 732 SEQADV 2Z3W MET A 27 UNP Q7MUW6 EXPRESSION TAG SEQADV 2Z3W ARG A 28 UNP Q7MUW6 EXPRESSION TAG SEQADV 2Z3W GLY A 29 UNP Q7MUW6 EXPRESSION TAG SEQADV 2Z3W SER A 30 UNP Q7MUW6 EXPRESSION TAG SEQADV 2Z3W HIS A 31 UNP Q7MUW6 EXPRESSION TAG SEQADV 2Z3W HIS A 32 UNP Q7MUW6 EXPRESSION TAG SEQADV 2Z3W HIS A 33 UNP Q7MUW6 EXPRESSION TAG SEQADV 2Z3W HIS A 34 UNP Q7MUW6 EXPRESSION TAG SEQADV 2Z3W HIS A 35 UNP Q7MUW6 EXPRESSION TAG SEQADV 2Z3W HIS A 36 UNP Q7MUW6 EXPRESSION TAG SEQADV 2Z3W GLY A 37 UNP Q7MUW6 EXPRESSION TAG SEQADV 2Z3W SER A 38 UNP Q7MUW6 EXPRESSION TAG SEQADV 2Z3W ALA A 636 UNP Q7MUW6 GLU 636 ENGINEERED MUTATION SEQRES 1 A 706 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER LEU SEQRES 2 A 706 MET PRO GLY GLY LYS GLU PHE TYR ASN PHE TYR PRO GLU SEQRES 3 A 706 TYR VAL VAL GLY LEU GLN TRP MET GLY ASP ASN TYR VAL SEQRES 4 A 706 PHE ILE GLU GLY ASP ASP LEU VAL PHE ASN LYS ALA ASN SEQRES 5 A 706 GLY LYS SER ALA GLN THR THR ARG PHE SER ALA ALA ASP SEQRES 6 A 706 LEU ASN ALA LEU MET PRO GLU GLY CYS LYS PHE GLN THR SEQRES 7 A 706 THR ASP ALA PHE PRO SER PHE ARG THR LEU ASP ALA GLY SEQRES 8 A 706 ARG GLY LEU VAL VAL LEU PHE THR GLN GLY GLY LEU VAL SEQRES 9 A 706 GLY PHE ASP MET LEU ALA ARG LYS VAL THR TYR LEU PHE SEQRES 10 A 706 ASP THR ASN GLU GLU THR ALA SER LEU ASP PHE SER PRO SEQRES 11 A 706 VAL GLY ASP ARG VAL ALA TYR VAL ARG ASN HIS ASN LEU SEQRES 12 A 706 TYR ILE ALA ARG GLY GLY LYS LEU GLY GLU GLY MET SER SEQRES 13 A 706 ARG ALA ILE ALA VAL THR ILE ASP GLY THR GLU THR LEU SEQRES 14 A 706 VAL TYR GLY GLN ALA VAL HIS GLN ARG GLU PHE GLY ILE SEQRES 15 A 706 GLU LYS GLY THR PHE TRP SER PRO LYS GLY SER CYS LEU SEQRES 16 A 706 ALA PHE TYR ARG MET ASP GLN SER MET VAL LYS PRO THR SEQRES 17 A 706 PRO ILE VAL ASP TYR HIS PRO LEU GLU ALA GLU SER LYS SEQRES 18 A 706 PRO LEU TYR TYR PRO MET ALA GLY THR PRO SER HIS HIS SEQRES 19 A 706 VAL THR VAL GLY ILE TYR HIS LEU ALA THR GLY LYS THR SEQRES 20 A 706 VAL TYR LEU GLN THR GLY GLU PRO LYS GLU LYS PHE LEU SEQRES 21 A 706 THR ASN LEU SER TRP SER PRO ASP GLU ASN ILE LEU TYR SEQRES 22 A 706 VAL ALA GLU VAL ASN ARG ALA GLN ASN GLU CYS LYS VAL SEQRES 23 A 706 ASN ALA TYR ASP ALA GLU THR GLY ARG PHE VAL ARG THR SEQRES 24 A 706 LEU PHE VAL GLU THR ASP LYS HIS TYR VAL GLU PRO LEU SEQRES 25 A 706 HIS PRO LEU THR PHE LEU PRO GLY SER ASN ASN GLN PHE SEQRES 26 A 706 ILE TRP GLN SER ARG ARG ASP GLY TRP ASN HIS LEU TYR SEQRES 27 A 706 LEU TYR ASP THR THR GLY ARG LEU ILE ARG GLN VAL THR SEQRES 28 A 706 LYS GLY GLU TRP GLU VAL THR ASN PHE ALA GLY PHE ASP SEQRES 29 A 706 PRO LYS GLY THR ARG LEU TYR PHE GLU SER THR GLU ALA SEQRES 30 A 706 SER PRO LEU GLU ARG HIS PHE TYR CYS ILE ASP ILE LYS SEQRES 31 A 706 GLY GLY LYS THR LYS ASP LEU THR PRO GLU SER GLY MET SEQRES 32 A 706 HIS ARG THR GLN LEU SER PRO ASP GLY SER ALA ILE ILE SEQRES 33 A 706 ASP ILE PHE GLN SER PRO THR VAL PRO ARG LYS VAL THR SEQRES 34 A 706 VAL THR ASN ILE GLY LYS GLY SER HIS THR LEU LEU GLU SEQRES 35 A 706 ALA LYS ASN PRO ASP THR GLY TYR ALA MET PRO GLU ILE SEQRES 36 A 706 ARG THR GLY THR ILE MET ALA ALA ASP GLY GLN THR PRO SEQRES 37 A 706 LEU TYR TYR LYS LEU THR MET PRO LEU HIS PHE ASP PRO SEQRES 38 A 706 ALA LYS LYS TYR PRO VAL ILE VAL TYR VAL TYR GLY GLY SEQRES 39 A 706 PRO HIS ALA GLN LEU VAL THR LYS THR TRP ARG SER SER SEQRES 40 A 706 VAL GLY GLY TRP ASP ILE TYR MET ALA GLN LYS GLY TYR SEQRES 41 A 706 ALA VAL PHE THR VAL ASP SER ARG GLY SER ALA ASN ARG SEQRES 42 A 706 GLY ALA ALA PHE GLU GLN VAL ILE HIS ARG ARG LEU GLY SEQRES 43 A 706 GLN THR GLU MET ALA ASP GLN MET CYS GLY VAL ASP PHE SEQRES 44 A 706 LEU LYS SER GLN SER TRP VAL ASP ALA ASP ARG ILE GLY SEQRES 45 A 706 VAL HIS GLY TRP SER TYR GLY GLY PHE MET THR THR ASN SEQRES 46 A 706 LEU MET LEU THR HIS GLY ASP VAL PHE LYS VAL GLY VAL SEQRES 47 A 706 ALA GLY GLY PRO VAL ILE ASP TRP ASN ARG TYR ALA ILE SEQRES 48 A 706 MET TYR GLY GLU ARG TYR PHE ASP ALA PRO GLN GLU ASN SEQRES 49 A 706 PRO GLU GLY TYR ASP ALA ALA ASN LEU LEU LYS ARG ALA SEQRES 50 A 706 GLY ASP LEU LYS GLY ARG LEU MET LEU ILE HIS GLY ALA SEQRES 51 A 706 ILE ASP PRO VAL VAL VAL TRP GLN HIS SER LEU LEU PHE SEQRES 52 A 706 LEU ASP ALA CYS VAL LYS ALA ARG THR TYR PRO ASP TYR SEQRES 53 A 706 TYR VAL TYR PRO SER HIS GLU HIS ASN VAL MET GLY PRO SEQRES 54 A 706 ASP ARG VAL HIS LEU TYR GLU THR ILE THR ARG TYR PHE SEQRES 55 A 706 THR ASP HIS LEU HET SO4 A 902 5 HET GOL A 901 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SO4 O4 S 2- FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *547(H2 O) HELIX 1 1 ALA A 89 MET A 96 1 8 HELIX 2 2 VAL A 201 GLU A 205 5 5 HELIX 3 3 GLY A 536 LYS A 544 1 9 HELIX 4 4 GLY A 560 VAL A 566 1 7 HELIX 5 5 GLY A 572 SER A 588 1 17 HELIX 6 6 SER A 603 HIS A 616 1 14 HELIX 7 7 ASP A 631 TYR A 635 5 5 HELIX 8 8 ALA A 636 ASP A 645 1 10 HELIX 9 9 ALA A 646 GLU A 649 5 4 HELIX 10 10 ASN A 650 ASN A 658 1 9 HELIX 11 11 LEU A 659 LEU A 666 5 8 HELIX 12 12 TRP A 683 ARG A 697 1 15 HELIX 13 13 PRO A 715 LEU A 732 1 18 SHEET 1 A 4 GLN A 58 MET A 60 0 SHEET 2 A 4 ASN A 63 GLU A 68 -1 O ASN A 63 N MET A 60 SHEET 3 A 4 ASP A 71 ASN A 75 -1 O VAL A 73 N PHE A 66 SHEET 4 A 4 THR A 85 SER A 88 -1 O THR A 85 N PHE A 74 SHEET 1 B 4 PHE A 111 ASP A 115 0 SHEET 2 B 4 LEU A 120 THR A 125 -1 O LEU A 120 N LEU A 114 SHEET 3 B 4 GLY A 128 ASP A 133 -1 O VAL A 130 N LEU A 123 SHEET 4 B 4 LYS A 138 PHE A 143 -1 O TYR A 141 N GLY A 131 SHEET 1 C 4 ASP A 153 PHE A 154 0 SHEET 2 C 4 ARG A 160 ARG A 165 -1 O ALA A 162 N ASP A 153 SHEET 3 C 4 ASN A 168 ARG A 173 -1 O ALA A 172 N VAL A 161 SHEET 4 C 4 ILE A 185 ALA A 186 -1 O ILE A 185 N ILE A 171 SHEET 1 D 3 LEU A 195 TYR A 197 0 SHEET 2 D 3 CYS A 220 ASP A 227 -1 O MET A 226 N VAL A 196 SHEET 3 D 3 THR A 212 TRP A 214 -1 N PHE A 213 O ALA A 222 SHEET 1 E 4 LEU A 195 TYR A 197 0 SHEET 2 E 4 CYS A 220 ASP A 227 -1 O MET A 226 N VAL A 196 SHEET 3 E 4 HIS A 260 HIS A 267 -1 O TYR A 266 N LEU A 221 SHEET 4 E 4 LYS A 272 TYR A 275 -1 O LYS A 272 N HIS A 267 SHEET 1 F 2 THR A 234 ASP A 238 0 SHEET 2 F 2 GLU A 245 LEU A 249 -1 O GLU A 245 N ASP A 238 SHEET 1 G 4 PHE A 285 TRP A 291 0 SHEET 2 G 4 ILE A 297 VAL A 303 -1 O TYR A 299 N SER A 290 SHEET 3 G 4 GLU A 309 ASP A 316 -1 O LYS A 311 N GLU A 302 SHEET 4 G 4 PHE A 322 THR A 330 -1 O LEU A 326 N VAL A 312 SHEET 1 H 4 THR A 342 PHE A 343 0 SHEET 2 H 4 GLN A 350 SER A 355 -1 O ILE A 352 N THR A 342 SHEET 3 H 4 HIS A 362 ASP A 367 -1 O TYR A 364 N TRP A 353 SHEET 4 H 4 LEU A 372 GLN A 375 -1 O ARG A 374 N LEU A 365 SHEET 1 I 4 VAL A 383 PHE A 389 0 SHEET 2 I 4 ARG A 395 SER A 400 -1 O TYR A 397 N GLY A 388 SHEET 3 I 4 HIS A 409 ASP A 414 -1 O TYR A 411 N PHE A 398 SHEET 4 I 4 LYS A 421 ASP A 422 -1 O LYS A 421 N CYS A 412 SHEET 1 J 4 MET A 429 LEU A 434 0 SHEET 2 J 4 ALA A 440 GLN A 446 -1 O GLN A 446 N MET A 429 SHEET 3 J 4 LYS A 453 ASN A 458 -1 O THR A 457 N ILE A 441 SHEET 4 J 4 SER A 463 GLU A 468 -1 O LEU A 466 N VAL A 454 SHEET 1 K 8 ILE A 481 MET A 487 0 SHEET 2 K 8 PRO A 494 THR A 500 -1 O LEU A 495 N ILE A 486 SHEET 3 K 8 ALA A 547 VAL A 551 -1 O VAL A 548 N THR A 500 SHEET 4 K 8 TYR A 511 TYR A 516 1 N ILE A 514 O ALA A 547 SHEET 5 K 8 VAL A 592 TRP A 602 1 O GLY A 598 N VAL A 515 SHEET 6 K 8 PHE A 620 GLY A 626 1 O LYS A 621 N ILE A 597 SHEET 7 K 8 ARG A 669 GLY A 675 1 O ARG A 669 N GLY A 623 SHEET 8 K 8 ASP A 701 TYR A 705 1 O ASP A 701 N LEU A 670 CISPEP 1 GLU A 280 PRO A 281 0 -3.26 CISPEP 2 GLY A 460 LYS A 461 0 3.71 SITE 1 AC1 5 ARG A 321 SER A 347 ASN A 349 GLN A 350 SITE 2 AC1 5 HOH A1048 SITE 1 AC2 7 TYR A 518 SER A 603 TYR A 604 TYR A 635 SITE 2 AC2 7 TYR A 639 VAL A 681 HOH A1030 CRYST1 149.709 149.709 160.943 90.00 90.00 120.00 P 63 2 2 12 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 0.006680 0.003856 0.000000 0.00000 SCALE2 0.000000 0.007713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006213 0.00000