HEADER HYDROLASE 30-AUG-09 3IU9 TITLE M. TUBERCULOSIS METHIONINE AMINOPEPTIDASE WITH NI INHIBITOR T07 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 3IU9 1 REMARK SEQADV LINK REVDAT 3 01-NOV-17 3IU9 1 REMARK REVDAT 2 16-FEB-10 3IU9 1 JRNL REVDAT 1 12-JAN-10 3IU9 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. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 32958 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1666 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) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2187 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.1760 REMARK 3 BIN FREE R VALUE SET COUNT : 102 REMARK 3 BIN FREE R VALUE : 0.2380 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 : 193 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.57 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): 0.097 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.692 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2238 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3061 ; 2.309 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 283 ; 6.363 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;36.966 ;23.723 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 337 ;12.761 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;21.947 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 350 ; 0.190 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1714 ; 0.014 ; 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 ; 1.302 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2293 ; 2.094 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 827 ; 3.392 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 768 ; 5.276 ; 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 3IU9 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_1000054871. 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 : 32971 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 : 9.100 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.17500 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 (%): 54.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, PH 5.5, 1.3 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 25.39700 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 25.39700 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 25.39700 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: 3930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 53.10800 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 91.98575 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -53.10800 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 91.98575 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 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 0.102 REMARK 500 TYR A 135 CE1 TYR A 135 CZ 0.080 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 16 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 16 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 51 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 55 NE - CZ - NH1 ANGL. DEV. = -4.4 DEGREES REMARK 500 GLU A 76 OE1 - CD - OE2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ASP A 118 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 MET A 240 CG - SD - CE ANGL. DEV. = 11.6 DEGREES REMARK 500 ARG A 262 NE - CZ - NH2 ANGL. DEV. = 3.3 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 -112.63 57.10 REMARK 500 ASP A 118 -156.49 -162.84 REMARK 500 GLN A 222 87.38 -152.09 REMARK 500 GLU A 238 54.40 -157.59 REMARK 500 TRP A 255 -50.23 -123.72 REMARK 500 THR A 283 54.11 -102.23 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 286 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 131 OD1 REMARK 620 2 ASP A 131 OD2 61.8 REMARK 620 3 ASP A 142 OD2 100.0 160.8 REMARK 620 4 GLU A 269 OE1 147.5 98.4 94.6 REMARK 620 5 GLU A 269 OE2 94.0 92.1 82.4 59.1 REMARK 620 6 T07 A 288 N4 109.2 90.9 101.9 95.8 154.9 REMARK 620 N 1 2 3 4 5 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 89.2 REMARK 620 3 GLU A 238 OE1 163.1 95.0 REMARK 620 4 GLU A 238 OE2 104.4 90.8 59.2 REMARK 620 5 GLU A 269 OE1 85.3 169.4 87.8 81.9 REMARK 620 6 T07 A 288 N2 104.7 100.0 90.8 149.1 90.2 REMARK 620 N 1 2 3 4 5 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 T07 A 288 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 289 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: 3IU8 RELATED DB: PDB DBREF 3IU9 A 2 285 UNP P0A5J2 AMPM_MYCTU 2 285 SEQADV 3IU9 MET A -2 UNP P0A5J2 EXPRESSION TAG SEQADV 3IU9 ALA A -1 UNP P0A5J2 EXPRESSION TAG SEQADV 3IU9 SER A 0 UNP P0A5J2 EXPRESSION TAG SEQADV 3IU9 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 T07 A 288 16 HET SO4 A 289 5 HET CL A 290 1 HETNAM NI NICKEL (II) ION HETNAM T07 5-[(2,4-DICHLOROBENZYL)SULFANYL]-4H-1,2,4-TRIAZOL-3- HETNAM 2 T07 AMINE HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 2 NI 2(NI 2+) FORMUL 4 T07 C9 H8 CL2 N4 S FORMUL 5 SO4 O4 S 2- FORMUL 6 CL CL 1- FORMUL 7 HOH *193(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 SER A 107 O ASN A 129 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 OD1 ASP A 131 NI NI A 286 1555 1555 2.18 LINK OD2 ASP A 131 NI NI A 286 1555 1555 2.13 LINK OD2 ASP A 142 NI NI A 286 1555 1555 2.01 LINK OD1 ASP A 142 NI NI A 287 1555 1555 2.02 LINK NE2 HIS A 205 NI NI A 287 1555 1555 2.14 LINK OE1 GLU A 238 NI NI A 287 1555 1555 2.24 LINK OE2 GLU A 238 NI NI A 287 1555 1555 2.14 LINK OE1 GLU A 269 NI NI A 286 1555 1555 2.10 LINK OE2 GLU A 269 NI NI A 286 1555 1555 2.16 LINK OE1 GLU A 269 NI NI A 287 1555 1555 2.26 LINK NI NI A 286 N4 T07 A 288 1555 1555 1.99 LINK NI NI A 287 N2 T07 A 288 1555 1555 2.05 SITE 1 AC1 5 ASP A 131 ASP A 142 GLU A 269 NI A 287 SITE 2 AC1 5 T07 A 288 SITE 1 AC2 6 ASP A 142 HIS A 205 GLU A 238 GLU A 269 SITE 2 AC2 6 NI A 286 T07 A 288 SITE 1 AC3 16 TYR A 27 SER A 93 THR A 94 TYR A 97 SITE 2 AC3 16 CYS A 105 HIS A 114 ASP A 131 THR A 133 SITE 3 AC3 16 ASP A 142 HIS A 205 PHE A 211 HIS A 212 SITE 4 AC3 16 GLU A 238 GLU A 269 NI A 286 NI A 287 SITE 1 AC4 5 ASN A 20 ARG A 200 HOH A 323 HOH A 361 SITE 2 AC4 5 HOH A 396 CRYST1 106.216 106.216 50.794 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 0.009415 0.005436 0.000000 0.00000 SCALE2 0.000000 0.010871 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019687 0.00000