HEADER HYDROLASE 30-AUG-09 3IU8 TITLE M. TUBERCULOSIS METHIONINE AMINOPEPTIDASE WITH NI INHIBITOR T03 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONINE AMINOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MAP, PEPTIDASE M; COMPND 5 EC: 3.4.11.18; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: MAP, MAPB, MT2929, MTV003.07C, RV2861C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEMEX-1 KEYWDS ENZYME-INHIBITOR COMPLEX, AMINOPEPTIDASE, COBALT, HYDROLASE, METAL- KEYWDS 2 BINDING, PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.Z.YE,J.P.LU REVDAT 4 06-SEP-23 3IU8 1 REMARK SEQADV LINK REVDAT 3 01-NOV-17 3IU8 1 REMARK REVDAT 2 16-FEB-10 3IU8 1 JRNL REVDAT 1 12-JAN-10 3IU8 0 JRNL AUTH J.P.LU,S.C.CHAI,Q.Z.YE JRNL TITL CATALYSIS AND INHIBITION OF MYCOBACTERIUM TUBERCULOSIS JRNL TITL 2 METHIONINE AMINOPEPTIDASE JRNL REF J.MED.CHEM. V. 53 1329 2010 JRNL REFN ISSN 0022-2623 JRNL PMID 20038112 JRNL DOI 10.1021/JM901624N REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 27534 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1385 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1882 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 115 REMARK 3 BIN FREE R VALUE : 0.2450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2166 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 162 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.116 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.113 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.238 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2236 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3057 ; 1.968 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 283 ; 6.249 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;39.054 ;23.723 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 337 ;12.367 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;22.176 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 350 ; 0.166 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1712 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1411 ; 1.193 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2293 ; 1.998 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 825 ; 3.446 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 764 ; 5.344 ; 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3IU8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000054870. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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, HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27549 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.15600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.5 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 0.71400 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 1YJ3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, PH 5.5, 1.4 M AMS, 15% REMARK 280 GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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 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 25.21350 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 25.21350 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 25.21350 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 52.86400 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 91.56313 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -52.86400 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 91.56313 REMARK 350 BIOMT3 3 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 445 LIES ON A SPECIAL POSITION. 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 -2 REMARK 465 ALA A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 48 CG GLU A 48 CD 0.096 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 4 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 16 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 185 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 185 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 MET A 240 CG - SD - CE ANGL. DEV. = 10.8 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 ASN A 109 -110.23 61.59 REMARK 500 ASP A 118 -159.30 -158.92 REMARK 500 GLN A 222 85.02 -152.89 REMARK 500 GLU A 238 53.97 -154.26 REMARK 500 THR A 283 55.14 -92.77 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 NI A 288 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 114 NE2 REMARK 620 2 T03 A 289 N1 134.2 REMARK 620 3 CL A 292 CL 103.6 109.8 REMARK 620 4 HOH A 447 O 103.0 100.6 100.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 286 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 131 OD1 REMARK 620 2 ASP A 131 OD2 57.4 REMARK 620 3 ASP A 142 OD2 102.6 156.9 REMARK 620 4 GLU A 269 OE2 113.4 86.3 92.7 REMARK 620 5 T03 A 289 N3 108.7 86.0 113.3 123.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 287 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 142 OD1 REMARK 620 2 HIS A 205 NE2 89.9 REMARK 620 3 GLU A 238 OE2 156.0 91.5 REMARK 620 4 GLU A 269 OE1 81.8 133.3 79.8 REMARK 620 5 T03 A 289 N2 93.5 105.1 109.2 121.1 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 NI A 286 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 288 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE T03 A 289 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 290 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 291 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 292 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XNZ RELATED DB: PDB REMARK 900 E. COLI METHIONINE AMINOPEPTIDASE COMPLEXED WITH THE SAME INHIBITOR REMARK 900 RELATED ID: 1YJ3 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH MET REMARK 900 RELATED ID: 3IU7 RELATED DB: PDB REMARK 900 RELATED ID: 3IU9 RELATED DB: PDB DBREF 3IU8 A 2 285 UNP P0A5J2 AMPM_MYCTU 2 285 SEQADV 3IU8 MET A -2 UNP P0A5J2 EXPRESSION TAG SEQADV 3IU8 ALA A -1 UNP P0A5J2 EXPRESSION TAG SEQADV 3IU8 SER A 0 UNP P0A5J2 EXPRESSION TAG SEQADV 3IU8 MET A 1 UNP P0A5J2 EXPRESSION TAG SEQRES 1 A 288 MET ALA SER MET PRO SER ARG THR ALA LEU SER PRO GLY SEQRES 2 A 288 VAL LEU SER PRO THR ARG PRO VAL PRO ASN TRP ILE ALA SEQRES 3 A 288 ARG PRO GLU TYR VAL GLY LYS PRO ALA ALA GLN GLU GLY SEQRES 4 A 288 SER GLU PRO TRP VAL GLN THR PRO GLU VAL ILE GLU LYS SEQRES 5 A 288 MET ARG VAL ALA GLY ARG ILE ALA ALA GLY ALA LEU ALA SEQRES 6 A 288 GLU ALA GLY LYS ALA VAL ALA PRO GLY VAL THR THR ASP SEQRES 7 A 288 GLU LEU ASP ARG ILE ALA HIS GLU TYR LEU VAL ASP ASN SEQRES 8 A 288 GLY ALA TYR PRO SER THR LEU GLY TYR LYS GLY PHE PRO SEQRES 9 A 288 LYS SER CYS CYS THR SER LEU ASN GLU VAL ILE CYS HIS SEQRES 10 A 288 GLY ILE PRO ASP SER THR VAL ILE THR ASP GLY ASP ILE SEQRES 11 A 288 VAL ASN ILE ASP VAL THR ALA TYR ILE GLY GLY VAL HIS SEQRES 12 A 288 GLY ASP THR ASN ALA THR PHE PRO ALA GLY ASP VAL ALA SEQRES 13 A 288 ASP GLU HIS ARG LEU LEU VAL ASP ARG THR ARG GLU ALA SEQRES 14 A 288 THR MET ARG ALA ILE ASN THR VAL LYS PRO GLY ARG ALA SEQRES 15 A 288 LEU SER VAL ILE GLY ARG VAL ILE GLU SER TYR ALA ASN SEQRES 16 A 288 ARG PHE GLY TYR ASN VAL VAL ARG ASP PHE THR GLY HIS SEQRES 17 A 288 GLY ILE GLY THR THR PHE HIS ASN GLY LEU VAL VAL LEU SEQRES 18 A 288 HIS TYR ASP GLN PRO ALA VAL GLU THR ILE MET GLN PRO SEQRES 19 A 288 GLY MET THR PHE THR ILE GLU PRO MET ILE ASN LEU GLY SEQRES 20 A 288 ALA LEU ASP TYR GLU ILE TRP ASP ASP GLY TRP THR VAL SEQRES 21 A 288 VAL THR LYS ASP ARG LYS TRP THR ALA GLN PHE GLU HIS SEQRES 22 A 288 THR LEU LEU VAL THR ASP THR GLY VAL GLU ILE LEU THR SEQRES 23 A 288 CYS LEU HET NI A 286 1 HET NI A 287 1 HET NI A 288 1 HET T03 A 289 14 HET SO4 A 290 5 HET CL A 291 1 HET CL A 292 1 HETNAM NI NICKEL (II) ION HETNAM T03 3-[(4-FLUOROBENZYL)SULFANYL]-4H-1,2,4-TRIAZOLE HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 2 NI 3(NI 2+) FORMUL 5 T03 C9 H8 F N3 S FORMUL 6 SO4 O4 S 2- FORMUL 7 CL 2(CL 1-) FORMUL 9 HOH *162(H2 O) HELIX 1 1 THR A 43 ALA A 67 1 25 HELIX 2 2 THR A 73 ASN A 88 1 16 HELIX 3 3 GLY A 96 PHE A 100 5 5 HELIX 4 4 ALA A 153 THR A 173 1 21 HELIX 5 5 SER A 181 ARG A 193 1 13 SHEET 1 A 3 TYR A 91 PRO A 92 0 SHEET 2 A 3 ILE A 127 ILE A 136 -1 O TYR A 135 N TYR A 91 SHEET 3 A 3 CYS A 105 LEU A 108 -1 N CYS A 105 O ASP A 131 SHEET 1 B 3 TYR A 91 PRO A 92 0 SHEET 2 B 3 ILE A 127 ILE A 136 -1 O TYR A 135 N TYR A 91 SHEET 3 B 3 VAL A 139 PRO A 148 -1 O THR A 143 N VAL A 132 SHEET 1 C 3 VAL A 111 CYS A 113 0 SHEET 2 C 3 VAL A 257 THR A 259 -1 O VAL A 257 N ILE A 112 SHEET 3 C 3 TYR A 248 ILE A 250 -1 N GLU A 249 O VAL A 258 SHEET 1 D 3 ASN A 197 VAL A 198 0 SHEET 2 D 3 MET A 240 ASN A 242 -1 O ASN A 242 N ASN A 197 SHEET 3 D 3 THR A 265 GLN A 267 -1 O ALA A 266 N ILE A 241 SHEET 1 E 2 GLY A 204 HIS A 205 0 SHEET 2 E 2 VAL A 216 VAL A 217 -1 O VAL A 217 N GLY A 204 SHEET 1 F 3 THR A 234 ILE A 237 0 SHEET 2 F 3 HIS A 270 VAL A 274 -1 O LEU A 272 N PHE A 235 SHEET 3 F 3 VAL A 279 ILE A 281 -1 O GLU A 280 N LEU A 273 LINK NE2 HIS A 114 NI NI A 288 1555 1555 2.05 LINK OD1 ASP A 131 NI NI A 286 1555 1555 2.07 LINK OD2 ASP A 131 NI NI A 286 1555 1555 2.48 LINK OD2 ASP A 142 NI NI A 286 1555 1555 1.98 LINK OD1 ASP A 142 NI NI A 287 1555 1555 2.10 LINK NE2 HIS A 205 NI NI A 287 1555 1555 2.03 LINK OE2 GLU A 238 NI NI A 287 1555 1555 1.97 LINK OE2 GLU A 269 NI NI A 286 1555 1555 1.93 LINK OE1 GLU A 269 NI NI A 287 1555 1555 1.87 LINK NI NI A 286 N3 T03 A 289 1555 1555 1.93 LINK NI NI A 287 N2 T03 A 289 1555 1555 1.98 LINK NI NI A 288 N1 T03 A 289 1555 1555 2.02 LINK NI NI A 288 CL CL A 292 1555 1555 2.36 LINK NI NI A 288 O HOH A 447 1555 1555 1.98 SITE 1 AC1 5 ASP A 131 ASP A 142 GLU A 269 NI A 287 SITE 2 AC1 5 T03 A 289 SITE 1 AC2 6 ASP A 142 HIS A 205 GLU A 238 GLU A 269 SITE 2 AC2 6 NI A 286 T03 A 289 SITE 1 AC3 4 HIS A 114 T03 A 289 CL A 292 HOH A 447 SITE 1 AC4 15 THR A 94 TYR A 97 CYS A 105 HIS A 114 SITE 2 AC4 15 ASP A 131 ASP A 142 HIS A 205 GLU A 238 SITE 3 AC4 15 TRP A 255 GLU A 269 NI A 286 NI A 287 SITE 4 AC4 15 NI A 288 CL A 292 HOH A 447 SITE 1 AC5 5 ASN A 20 ARG A 200 HOH A 350 HOH A 451 SITE 2 AC5 5 HOH A 452 SITE 1 AC6 2 ARG A 169 ARG A 193 SITE 1 AC7 3 HIS A 114 NI A 288 T03 A 289 CRYST1 105.728 105.728 50.427 90.00 90.00 120.00 P 63 6 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 0.009458 0.005461 0.000000 0.00000 SCALE2 0.000000 0.010921 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019831 0.00000