PDB Short entry for 3B3T HEADER HYDROLASE 22-OCT-07 3B3T TITLE CRYSTAL STRUCTURE OF THE D118N MUTANT OF THE AMINOPEPTIDASE FROM TITLE 2 VIBRIO PROTEOLYTICUS 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 7 30-AUG-23 3B3T 1 REMARK REVDAT 6 20-OCT-21 3B3T 1 REMARK SEQADV LINK REVDAT 5 25-OCT-17 3B3T 1 REMARK REVDAT 4 24-FEB-09 3B3T 1 VERSN REVDAT 3 12-AUG-08 3B3T 1 JRNL REVDAT 2 19-FEB-08 3B3T 1 AUTHOR JRNL REVDAT 1 27-NOV-07 3B3T 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. 1.17 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) : 1.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 102258 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) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.161 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5101 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) : 1.17 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6785 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 REMARK 3 BIN FREE R VALUE SET COUNT : 356 REMARK 3 BIN FREE R VALUE : 0.2260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2211 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 292 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.39 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) : -0.02000 REMARK 3 B12 (A**2) : 0.01000 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): 0.032 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.032 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.018 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.856 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2399 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1521 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3287 ; 1.617 ; 1.930 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3743 ; 0.968 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 318 ; 6.114 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;36.091 ;25.421 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 371 ;11.263 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;22.371 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 362 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2808 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 474 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 561 ; 0.242 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1764 ; 0.201 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1288 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1175 ; 0.090 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 198 ; 0.191 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 7 ; 0.050 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 30 ; 0.423 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 41 ; 0.371 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.179 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 2 ; 1.620 ; 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): 1540 ; 1.532 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 618 ; 0.851 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2494 ; 2.209 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 859 ; 3.047 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 793 ; 4.328 ; 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): 3935 ; 1.525 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 297 ; 9.694 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3857 ; 5.079 ; 3.000 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 : 1.40 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 3B3T 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_1000045043. 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 : 102258 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.170 REMARK 200 RESOLUTION RANGE LOW (A) : 42.000 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 (%): 50.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 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 30.33633 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 60.67267 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 45.50450 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 75.84083 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 15.16817 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 30.33633 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 60.67267 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 75.84083 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 45.50450 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 15.16817 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 317 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 424 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 392 O HOH A 573 1.75 REMARK 500 OE1 GLN A 44 O HOH A 585 1.85 REMARK 500 O HOH A 396 O HOH A 581 2.00 REMARK 500 O HOH A 348 O HOH A 566 2.09 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 296 O HOH A 300 10555 0.73 REMARK 500 NA NA A 295 O HOH A 304 11655 0.85 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 254 NE - CZ - NH1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 254 NE - CZ - NH2 ANGL. DEV. = -5.4 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 MET A 180 97.91 77.89 REMARK 500 SER A 265 -108.29 -98.97 REMARK 500 SER A 265 -139.05 -105.90 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 NA A 294 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 74 OD1 REMARK 620 2 HOH A 385 O 102.9 REMARK 620 3 HOH A 506 O 87.3 87.0 REMARK 620 4 HOH A 540 O 86.8 87.7 171.1 REMARK 620 5 HOH A 569 O 82.0 168.1 82.3 103.5 REMARK 620 N 1 2 3 4 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 96.4 REMARK 620 3 ASP A 179 OD1 95.1 94.3 REMARK 620 4 ASP A 179 OD2 86.5 152.2 58.0 REMARK 620 5 ILE A 299 OXT 99.5 92.2 163.3 114.6 REMARK 620 6 ILE A 299 N 158.6 104.3 88.7 77.7 74.8 REMARK 620 N 1 2 3 4 5 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 157.4 REMARK 620 3 GLU A 152 OE2 99.2 58.5 REMARK 620 4 HIS A 256 NE2 92.3 92.6 111.8 REMARK 620 5 ILE A 299 OXT 96.3 95.1 108.3 136.9 REMARK 620 N 1 2 3 4 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 NA 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 SCN A 297 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN A 298 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ILE A 299 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: 3B3V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF S228A MUTANT OF AMINOPEPTIDASE FROM VIBRIO REMARK 900 PROTEOLYTICUS REMARK 900 RELATED ID: 3B3W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF S228A MUTANT OF AMINOPEPTIDASE FROM VIBRIO REMARK 900 PROTEOLYTICUS IN COMPLEX WITH LEUCINE DBREF 3B3T A 1 291 UNP Q01693 AMPX_VIBPR 107 397 SEQADV 3B3T ASN A 118 UNP Q01693 ASP 224 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 ASN 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 SER 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 NA A 294 1 HET NA A 295 1 HET NA A 296 1 HET SCN A 297 3 HET SCN A 298 3 HET ILE A 299 9 HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM SCN THIOCYANATE ION HETNAM ILE ISOLEUCINE FORMUL 2 ZN 2(ZN 2+) FORMUL 4 NA 3(NA 1+) FORMUL 7 SCN 2(C N S 1-) FORMUL 9 ILE C6 H13 N O2 FORMUL 10 HOH *292(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 SER A 31 1 14 HELIX 4 4 THR A 39 SER A 57 1 19 HELIX 5 5 ASN 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 HIS A 70 0 SHEET 2 A 6 TYR A 73 ILE A 82 -1 O SER A 77 N VAL A 68 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 92 O ALA A 144 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 2.03 LINK OD1 ASN A 74 NA NA A 294 1555 1555 2.41 LINK NE2 HIS A 97 ZN ZN A 293 1555 1555 2.06 LINK OD2 ASP A 117 ZN ZN A 292 1555 1555 2.02 LINK OD1 ASP A 117 ZN ZN A 293 1555 1555 2.00 LINK OE1 GLU A 152 ZN ZN A 292 1555 1555 2.35 LINK OE2 GLU A 152 ZN ZN A 292 1555 1555 2.04 LINK OD1 ASP A 179 ZN ZN A 293 1555 1555 2.12 LINK OD2 ASP A 179 ZN ZN A 293 1555 1555 2.37 LINK NE2 HIS A 256 ZN ZN A 292 1555 1555 1.99 LINK ZN ZN A 292 OXT ILE A 299 1555 1555 2.00 LINK ZN ZN A 293 OXT ILE A 299 1555 1555 2.17 LINK ZN ZN A 293 N ILE A 299 1555 1555 2.12 LINK NA NA A 294 O HOH A 385 1555 1555 2.32 LINK NA NA A 294 O HOH A 506 1555 1555 2.38 LINK NA NA A 294 O HOH A 540 1555 1555 2.36 LINK NA NA A 294 O HOH A 569 1555 1555 2.51 CISPEP 1 ASP A 117 ASN A 118 0 3.24 SITE 1 AC1 5 ASP A 117 GLU A 152 HIS A 256 ZN A 293 SITE 2 AC1 5 ILE A 299 SITE 1 AC2 5 HIS A 97 ASP A 117 ASP A 179 ZN A 292 SITE 2 AC2 5 ILE A 299 SITE 1 AC3 6 SER A 51 ASN A 74 HOH A 385 HOH A 506 SITE 2 AC3 6 HOH A 540 HOH A 569 SITE 1 AC4 3 SER A 71 GLY A 72 HOH A 304 SITE 1 AC5 2 THR A 258 HOH A 580 SITE 1 AC6 6 THR A 194 SER A 199 THR A 202 GLN A 203 SITE 2 AC6 6 LEU A 262 HOH A 422 SITE 1 AC7 4 ALA A 12 TRP A 13 HOH A 354 HOH A 397 SITE 1 AC8 16 HIS A 97 ASP A 117 GLU A 151 GLU A 152 SITE 2 AC8 16 ASP A 179 MET A 180 CYS A 227 PHE A 248 SITE 3 AC8 16 TYR A 251 ILE A 255 HIS A 256 ZN A 292 SITE 4 AC8 16 ZN A 293 HOH A 392 HOH A 439 HOH A 573 CRYST1 109.294 109.294 91.009 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 0.009150 0.005283 0.000000 0.00000 SCALE2 0.000000 0.010565 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010988 0.00000