HEADER HYDROLASE 22-OCT-07 3B3W TITLE CRYSTAL STRUCTURE OF THE S228A MUTANT OF THE AMINOPEPTIDASE FROM TITLE 2 VIBRIO PROTEOLYTICUS IN COMPLEX WITH LEUCINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIAL LEUCYL AMINOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 107-397; COMPND 5 EC: 3.4.11.10; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PROTEOLYTICUS; SOURCE 3 ORGANISM_TAXID: 671; SOURCE 4 STRAIN: DSM 30189 / IFO 13287 / LMG 3772 / NCIMB 1326; SOURCE 5 ATCC: 15338; SOURCE 6 GENE: AAP; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS ALPHA BETA, AMINOPEPTIDASE, HYDROLASE, METAL-BINDING, PROTEASE, KEYWDS 2 SECRETED, ZINC, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR N.J.ATAIE,Q.Q.HOANG,M.P.D.ZAHNISER,A.MILNE,G.A.PETSKO,D.RINGE REVDAT 8 30-OCT-24 3B3W 1 REMARK REVDAT 7 30-AUG-23 3B3W 1 REMARK REVDAT 6 20-OCT-21 3B3W 1 REMARK SEQADV LINK REVDAT 5 25-OCT-17 3B3W 1 REMARK REVDAT 4 24-FEB-09 3B3W 1 VERSN REVDAT 3 12-AUG-08 3B3W 1 JRNL REVDAT 2 19-FEB-08 3B3W 1 AUTHOR JRNL REVDAT 1 27-NOV-07 3B3W 0 JRNL AUTH N.J.ATAIE,Q.Q.HOANG,M.P.ZAHNISER,Y.TU,A.MILNE,G.A.PETSKO, JRNL AUTH 2 D.RINGE JRNL TITL ZINC COORDINATION GEOMETRY AND LIGAND BINDING AFFINITY: THE JRNL TITL 2 STRUCTURAL AND KINETIC ANALYSIS OF THE SECOND-SHELL SERINE JRNL TITL 3 228 RESIDUE AND THE METHIONINE 180 RESIDUE OF THE JRNL TITL 4 AMINOPEPTIDASE FROM VIBRIO PROTEOLYTICUS. JRNL REF BIOCHEMISTRY V. 47 7673 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18576673 JRNL DOI 10.1021/BI702188E REMARK 2 REMARK 2 RESOLUTION. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 30654 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1574 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2107 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.3670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2210 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 261 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 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): 0.129 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.791 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2276 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3106 ; 1.463 ; 1.930 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 292 ; 6.270 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 103 ;36.679 ;25.631 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 342 ;13.990 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;23.200 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 348 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1763 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1209 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1585 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 220 ; 0.154 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.191 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 34 ; 0.275 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 29 ; 0.390 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 3 ; 0.612 ; 0.200 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): 1457 ; 0.838 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2341 ; 1.445 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 819 ; 2.269 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 764 ; 3.492 ; 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3B3W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000045046. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90010 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30654 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 14.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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) : 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1AMP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, KSCN, NACL, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 30.54200 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 61.08400 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 45.81300 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 76.35500 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 15.27100 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 30.54200 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 61.08400 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 76.35500 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 45.81300 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 15.27100 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 300 REMARK: AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS REMARK 300 UNKNOWN. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 346 LIES ON A SPECIAL POSITION. 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 451 O HOH A 461 1.91 REMARK 500 O HOH A 473 O HOH A 546 2.09 REMARK 500 O HOH A 505 O HOH A 513 2.15 REMARK 500 O HOH A 449 O HOH A 517 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NA NA A 295 NA NA A 296 5554 1.35 REMARK 500 O HOH A 337 O HOH A 404 10555 1.59 REMARK 500 O HOH A 332 O HOH A 337 10555 1.81 REMARK 500 O HOH A 332 O HOH A 332 10555 2.14 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 156 NE - CZ - NH2 ANGL. DEV. = -3.1 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 GLU A 86 -41.70 -131.29 REMARK 500 HIS A 105 -44.12 107.88 REMARK 500 MET A 180 98.94 74.62 REMARK 500 ASN A 252 107.41 -36.06 REMARK 500 SER A 265 -136.46 -96.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 104 HIS A 105 30.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 293 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 97 NE2 REMARK 620 2 ASP A 117 OD1 100.7 REMARK 620 3 ASP A 179 OD1 102.5 95.0 REMARK 620 4 LEU A 297 O 99.5 88.1 156.8 REMARK 620 5 LEU A 297 N 125.5 130.1 92.6 68.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 292 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 117 OD2 REMARK 620 2 GLU A 152 OE1 159.9 REMARK 620 3 GLU A 152 OE2 98.9 61.2 REMARK 620 4 HIS A 256 NE2 96.0 93.2 108.5 REMARK 620 5 LEU A 297 O 91.8 91.1 104.6 144.3 REMARK 620 6 LEU A 297 OXT 109.5 89.1 147.3 84.9 59.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 296 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 218 OH REMARK 620 2 HOH A 387 O 96.9 REMARK 620 3 HOH A 502 O 68.8 145.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 295 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 347 O REMARK 620 2 HOH A 348 O 106.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 292 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN A 294 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LEU A 297 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3B35 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF M180A MUTANT OF AMINOPEPTIDASE FROM VIBRIO REMARK 900 PROTEOLYTICUS REMARK 900 RELATED ID: 3B3C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF M180A MUTANT OF AMINOPEPTIDASE FROM VIBRIO REMARK 900 PROTEOLYTICUS IN COMPLEX WITH LEUCINE PHOSPHONIC ACID REMARK 900 RELATED ID: 3B3S RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF M180A MUTANT OF AMINOPEPTIDASE FROM VIBRIO REMARK 900 PROTEOLYTICUS IN COMPLEX WITH LEUCINE REMARK 900 RELATED ID: 3B3T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D118N MUTANT OF AMINOPEPTIDASE FROM VIBRIO REMARK 900 PROTEOLYTICUS REMARK 900 RELATED ID: 3B3V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF S228A MUTANT OF AMINOPEPTIDASE FROM VIBRIO REMARK 900 PROTEOLYTICUS DBREF 3B3W A 1 291 UNP Q01693 AMPX_VIBPR 107 397 SEQADV 3B3W ALA A 228 UNP Q01693 SER 334 ENGINEERED MUTATION SEQRES 1 A 291 MET PRO PRO ILE THR GLN GLN ALA THR VAL THR ALA TRP SEQRES 2 A 291 LEU PRO GLN VAL ASP ALA SER GLN ILE THR GLY THR ILE SEQRES 3 A 291 SER SER LEU GLU SER PHE THR ASN ARG PHE TYR THR THR SEQRES 4 A 291 THR SER GLY ALA GLN ALA SER ASP TRP ILE ALA SER GLU SEQRES 5 A 291 TRP GLN ALA LEU SER ALA SER LEU PRO ASN ALA SER VAL SEQRES 6 A 291 LYS GLN VAL SER HIS SER GLY TYR ASN GLN LYS SER VAL SEQRES 7 A 291 VAL MET THR ILE THR GLY SER GLU ALA PRO ASP GLU TRP SEQRES 8 A 291 ILE VAL ILE GLY GLY HIS LEU ASP SER THR ILE GLY SER SEQRES 9 A 291 HIS THR ASN GLU GLN SER VAL ALA PRO GLY ALA ASP ASP SEQRES 10 A 291 ASP ALA SER GLY ILE ALA ALA VAL THR GLU VAL ILE ARG SEQRES 11 A 291 VAL LEU SER GLU ASN ASN PHE GLN PRO LYS ARG SER ILE SEQRES 12 A 291 ALA PHE MET ALA TYR ALA ALA GLU GLU VAL GLY LEU ARG SEQRES 13 A 291 GLY SER GLN ASP LEU ALA ASN GLN TYR LYS SER GLU GLY SEQRES 14 A 291 LYS ASN VAL VAL SER ALA LEU GLN LEU ASP MET THR ASN SEQRES 15 A 291 TYR LYS GLY SER ALA GLN ASP VAL VAL PHE ILE THR ASP SEQRES 16 A 291 TYR THR ASP SER ASN PHE THR GLN TYR LEU THR GLN LEU SEQRES 17 A 291 MET ASP GLU TYR LEU PRO SER LEU THR TYR GLY PHE ASP SEQRES 18 A 291 THR CYS GLY TYR ALA CYS ALA ASP HIS ALA SER TRP HIS SEQRES 19 A 291 ASN ALA GLY TYR PRO ALA ALA MET PRO PHE GLU SER LYS SEQRES 20 A 291 PHE ASN ASP TYR ASN PRO ARG ILE HIS THR THR GLN ASP SEQRES 21 A 291 THR LEU ALA ASN SER ASP PRO THR GLY SER HIS ALA LYS SEQRES 22 A 291 LYS PHE THR GLN LEU GLY LEU ALA TYR ALA ILE GLU MET SEQRES 23 A 291 GLY SER ALA THR GLY HET ZN A 292 1 HET ZN A 293 1 HET SCN A 294 3 HET NA A 295 1 HET NA A 296 1 HET LEU A 297 9 HETNAM ZN ZINC ION HETNAM SCN THIOCYANATE ION HETNAM NA SODIUM ION HETNAM LEU LEUCINE FORMUL 2 ZN 2(ZN 2+) FORMUL 4 SCN C N S 1- FORMUL 5 NA 2(NA 1+) FORMUL 7 LEU C6 H13 N O2 FORMUL 8 HOH *261(H2 O) HELIX 1 1 GLN A 6 LEU A 14 1 9 HELIX 2 2 PRO A 15 VAL A 17 5 3 HELIX 3 3 ASP A 18 GLU A 30 1 13 HELIX 4 4 THR A 39 ALA A 58 1 20 HELIX 5 5 ASP A 118 ASN A 135 1 18 HELIX 6 6 ALA A 150 GLY A 154 5 5 HELIX 7 7 LEU A 155 GLU A 168 1 14 HELIX 8 8 ASP A 198 LEU A 213 1 16 HELIX 9 9 ASP A 229 ALA A 236 1 8 HELIX 10 10 LYS A 247 TYR A 251 5 5 HELIX 11 11 THR A 261 SER A 265 5 5 HELIX 12 12 GLY A 269 ALA A 289 1 21 SHEET 1 A 6 ALA A 63 VAL A 68 0 SHEET 2 A 6 SER A 77 ILE A 82 -1 O THR A 81 N SER A 64 SHEET 3 A 6 ARG A 141 TYR A 148 -1 O PHE A 145 N MET A 80 SHEET 4 A 6 ALA A 87 HIS A 97 1 N ILE A 94 O MET A 146 SHEET 5 A 6 ASN A 171 GLN A 177 1 O ASN A 171 N TRP A 91 SHEET 6 A 6 ALA A 240 ALA A 241 1 O ALA A 241 N GLN A 177 SHEET 1 B 3 TYR A 218 ASP A 221 0 SHEET 2 B 3 VAL A 190 ILE A 193 1 N PHE A 192 O GLY A 219 SHEET 3 B 3 PRO A 243 PHE A 244 -1 O PHE A 244 N VAL A 191 SSBOND 1 CYS A 223 CYS A 227 1555 1555 2.05 LINK NE2 HIS A 97 ZN ZN A 293 1555 1555 2.10 LINK OD2 ASP A 117 ZN ZN A 292 1555 1555 2.02 LINK OD1 ASP A 117 ZN ZN A 293 1555 1555 2.06 LINK OE1 GLU A 152 ZN ZN A 292 1555 1555 2.25 LINK OE2 GLU A 152 ZN ZN A 292 1555 1555 2.03 LINK OD1 ASP A 179 ZN ZN A 293 1555 1555 2.04 LINK OH TYR A 218 NA NA A 296 1555 1555 2.64 LINK NE2 HIS A 256 ZN ZN A 292 1555 1555 2.00 LINK ZN ZN A 292 O LEU A 297 1555 1555 1.98 LINK ZN ZN A 292 OXT LEU A 297 1555 1555 2.32 LINK ZN ZN A 293 O LEU A 297 1555 1555 2.29 LINK ZN ZN A 293 N LEU A 297 1555 1555 2.32 LINK NA NA A 295 O HOH A 347 1555 1555 2.41 LINK NA NA A 295 O HOH A 348 1555 1555 2.09 LINK NA NA A 296 O HOH A 387 1555 1555 2.49 LINK NA NA A 296 O HOH A 502 1555 1555 2.71 CISPEP 1 ASP A 117 ASP A 118 0 -2.07 SITE 1 AC1 4 ASP A 117 GLU A 152 HIS A 256 LEU A 297 SITE 1 AC2 4 HIS A 97 ASP A 117 ASP A 179 LEU A 297 SITE 1 AC3 6 THR A 194 SER A 199 THR A 202 GLN A 203 SITE 2 AC3 6 PRO A 267 HOH A 506 SITE 1 AC4 6 TYR A 218 NA A 296 HOH A 347 HOH A 348 SITE 2 AC4 6 HOH A 387 HOH A 502 SITE 1 AC5 8 THR A 206 ASP A 210 TYR A 218 NA A 295 SITE 2 AC5 8 HOH A 310 HOH A 347 HOH A 387 HOH A 502 SITE 1 AC6 11 HIS A 97 ASP A 117 GLU A 151 GLU A 152 SITE 2 AC6 11 ASP A 179 TYR A 225 CYS A 227 HIS A 256 SITE 3 AC6 11 ZN A 292 ZN A 293 HOH A 360 CRYST1 110.549 110.549 91.626 90.00 90.00 120.00 P 61 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 0.009046 0.005223 0.000000 0.00000 SCALE2 0.000000 0.010445 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010914 0.00000