HEADER HYDROLASE/HYDROLASE INHIBITOR 11-NOV-10 3PKA TITLE M. TUBERCULOSIS METAP WITH BENGAMIDE ANALOG Y02, IN MN FORM 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEMEX-1 KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Q.Z.YE,J.P.LU REVDAT 4 21-FEB-24 3PKA 1 REMARK LINK REVDAT 3 29-MAY-13 3PKA 1 HETNAM REVDAT 2 13-JUL-11 3PKA 1 JRNL REVDAT 1 20-APR-11 3PKA 0 JRNL AUTH J.P.LU,X.H.YUAN,H.YUAN,W.L.WANG,B.WAN,S.G.FRANZBLAU,Q.Z.YE JRNL TITL INHIBITION OF MYCOBACTERIUM TUBERCULOSIS METHIONINE JRNL TITL 2 AMINOPEPTIDASES BY BENGAMIDE DERIVATIVES. JRNL REF CHEMMEDCHEM V. 6 1041 2011 JRNL REFN ISSN 1860-7179 JRNL PMID 21465667 JRNL DOI 10.1002/CMDC.201100003 REMARK 2 REMARK 2 RESOLUTION. 1.25 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 89125 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4471 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) : 1.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6185 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE SET COUNT : 330 REMARK 3 BIN FREE R VALUE : 0.2360 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 : 38 REMARK 3 SOLVENT ATOMS : 223 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.85 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.023 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.509 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2251 ; 0.033 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3080 ; 2.513 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 283 ; 6.306 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;36.183 ;23.723 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 337 ;10.629 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;21.649 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 355 ; 0.168 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1716 ; 0.015 ; 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): 1413 ; 1.222 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2296 ; 2.031 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 838 ; 3.049 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 784 ; 4.493 ; 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 3PKA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062475. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-10 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-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 89260 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 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 (%) : 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, PH 5.5, 1.3 M AMS, 10% 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 25.19750 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 25.19750 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 25.19750 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: 4790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 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 -106.00300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -53.00150 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -91.80129 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 488 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 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 THR A 5 CA THR A 5 CB 0.203 REMARK 500 VAL A 132 CB VAL A 132 CG1 -0.332 REMARK 500 GLU A 188 CD GLU A 188 OE1 0.067 REMARK 500 PHE A 194 CB PHE A 194 CG -0.104 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 CG - CD - NE ANGL. DEV. = 15.9 DEGREES REMARK 500 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 THR A 5 OG1 - CB - CG2 ANGL. DEV. = -14.8 DEGREES REMARK 500 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 16 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 51 NE - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 55 NE - CZ - NH1 ANGL. DEV. = -5.4 DEGREES REMARK 500 GLU A 76 OE1 - CD - OE2 ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG A 79 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 VAL A 86 CG1 - CB - CG2 ANGL. DEV. = 12.4 DEGREES REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ASP A 87 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 118 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP A 154 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 154 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 162 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 169 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 185 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 200 NE - CZ - NH1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 200 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 PHE A 202 CB - CG - CD1 ANGL. DEV. = -5.0 DEGREES REMARK 500 PHE A 211 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 PHE A 211 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ASP A 247 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 262 NE - CZ - NH2 ANGL. DEV. = 4.4 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 ASN A 109 -112.47 57.43 REMARK 500 ASP A 118 -160.38 -163.75 REMARK 500 GLU A 238 49.61 -146.76 REMARK 500 THR A 283 55.26 -104.78 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 MN A 287 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 131 OD1 REMARK 620 2 ASP A 131 OD2 58.5 REMARK 620 3 ASP A 142 OD2 96.3 153.4 REMARK 620 4 GLU A 269 OE2 106.6 90.2 89.3 REMARK 620 5 Y02 A 288 O1 82.5 86.9 98.9 167.1 REMARK 620 6 Y02 A 288 O3 144.3 92.8 113.8 93.1 74.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 286 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 142 OD1 REMARK 620 2 HIS A 205 NE2 93.4 REMARK 620 3 GLU A 238 OE2 156.4 87.5 REMARK 620 4 GLU A 269 OE1 83.1 118.7 75.8 REMARK 620 5 Y02 A 288 O3 100.2 150.2 90.2 89.3 REMARK 620 6 Y02 A 288 O2 110.3 78.9 93.1 158.0 71.6 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 MN A 286 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE Y02 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: 3IU7 RELATED DB: PDB REMARK 900 SAME PROTEIN WITH A DIFFERENT LIGAND REMARK 900 RELATED ID: 3IU8 RELATED DB: PDB REMARK 900 SAME PROTEIN WITH A DIFFERENT LIGAND REMARK 900 RELATED ID: 3IU9 RELATED DB: PDB REMARK 900 SAME PROTEIN WITH A DIFFERENT LIGAND REMARK 900 RELATED ID: 3PKE RELATED DB: PDB REMARK 900 RELATED ID: 3PKB RELATED DB: PDB REMARK 900 RELATED ID: 3PKC RELATED DB: PDB REMARK 900 RELATED ID: 3PKD RELATED DB: PDB DBREF 3PKA A 1 285 UNP P0A5J2 AMPM_MYCTU 1 285 SEQRES 1 A 285 MET PRO SER ARG THR ALA LEU SER PRO GLY VAL LEU SER SEQRES 2 A 285 PRO THR ARG PRO VAL PRO ASN TRP ILE ALA ARG PRO GLU SEQRES 3 A 285 TYR VAL GLY LYS PRO ALA ALA GLN GLU GLY SER GLU PRO SEQRES 4 A 285 TRP VAL GLN THR PRO GLU VAL ILE GLU LYS MET ARG VAL SEQRES 5 A 285 ALA GLY ARG ILE ALA ALA GLY ALA LEU ALA GLU ALA GLY SEQRES 6 A 285 LYS ALA VAL ALA PRO GLY VAL THR THR ASP GLU LEU ASP SEQRES 7 A 285 ARG ILE ALA HIS GLU TYR LEU VAL ASP ASN GLY ALA TYR SEQRES 8 A 285 PRO SER THR LEU GLY TYR LYS GLY PHE PRO LYS SER CYS SEQRES 9 A 285 CYS THR SER LEU ASN GLU VAL ILE CYS HIS GLY ILE PRO SEQRES 10 A 285 ASP SER THR VAL ILE THR ASP GLY ASP ILE VAL ASN ILE SEQRES 11 A 285 ASP VAL THR ALA TYR ILE GLY GLY VAL HIS GLY ASP THR SEQRES 12 A 285 ASN ALA THR PHE PRO ALA GLY ASP VAL ALA ASP GLU HIS SEQRES 13 A 285 ARG LEU LEU VAL ASP ARG THR ARG GLU ALA THR MET ARG SEQRES 14 A 285 ALA ILE ASN THR VAL LYS PRO GLY ARG ALA LEU SER VAL SEQRES 15 A 285 ILE GLY ARG VAL ILE GLU SER TYR ALA ASN ARG PHE GLY SEQRES 16 A 285 TYR ASN VAL VAL ARG ASP PHE THR GLY HIS GLY ILE GLY SEQRES 17 A 285 THR THR PHE HIS ASN GLY LEU VAL VAL LEU HIS TYR ASP SEQRES 18 A 285 GLN PRO ALA VAL GLU THR ILE MET GLN PRO GLY MET THR SEQRES 19 A 285 PHE THR ILE GLU PRO MET ILE ASN LEU GLY ALA LEU ASP SEQRES 20 A 285 TYR GLU ILE TRP ASP ASP GLY TRP THR VAL VAL THR LYS SEQRES 21 A 285 ASP ARG LYS TRP THR ALA GLN PHE GLU HIS THR LEU LEU SEQRES 22 A 285 VAL THR ASP THR GLY VAL GLU ILE LEU THR CYS LEU HET MN A 286 1 HET MN A 287 1 HET Y02 A 288 30 HET SO4 A 289 5 HET CL A 290 1 HETNAM MN MANGANESE (II) ION HETNAM Y02 (2R,3R,4S,5R,6E)-3,4,5-TRIHYDROXY-2-METHOXY-8,8- HETNAM 2 Y02 DIMETHYL-N-[2-(2,4,6-TRIMETHYLPHENOXY)ETHYL]NON-6- HETNAM 3 Y02 ENAMIDE HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 2 MN 2(MN 2+) FORMUL 4 Y02 C23 H37 N O6 FORMUL 5 SO4 O4 S 2- FORMUL 6 CL CL 1- FORMUL 7 HOH *223(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 PHE A 147 N VAL A 128 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 MN MN A 287 1555 1555 2.19 LINK OD2 ASP A 131 MN MN A 287 1555 1555 2.31 LINK OD1 ASP A 142 MN MN A 286 1555 1555 2.13 LINK OD2 ASP A 142 MN MN A 287 1555 1555 2.11 LINK NE2 HIS A 205 MN MN A 286 1555 1555 2.15 LINK OE2 GLU A 238 MN MN A 286 1555 1555 2.24 LINK OE1 GLU A 269 MN MN A 286 1555 1555 2.28 LINK OE2 GLU A 269 MN MN A 287 1555 1555 2.12 LINK MN MN A 286 O3 Y02 A 288 1555 1555 2.17 LINK MN MN A 286 O2 Y02 A 288 1555 1555 2.38 LINK MN MN A 287 O1 Y02 A 288 1555 1555 2.14 LINK MN MN A 287 O3 Y02 A 288 1555 1555 2.21 SITE 1 AC1 6 ASP A 142 HIS A 205 GLU A 238 GLU A 269 SITE 2 AC1 6 MN A 287 Y02 A 288 SITE 1 AC2 5 ASP A 131 ASP A 142 GLU A 269 MN A 286 SITE 2 AC2 5 Y02 A 288 SITE 1 AC3 17 GLU A 35 GLY A 36 TYR A 97 CYS A 105 SITE 2 AC3 17 HIS A 114 ASP A 131 ASP A 142 THR A 203 SITE 3 AC3 17 HIS A 205 PHE A 211 HIS A 212 GLU A 238 SITE 4 AC3 17 GLU A 269 MN A 286 MN A 287 HOH A 341 SITE 5 AC3 17 HOH A 397 SITE 1 AC4 3 ASN A 20 ARG A 200 HOH A 301 CRYST1 106.003 106.003 50.395 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 0.009434 0.005447 0.000000 0.00000 SCALE2 0.000000 0.010893 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019843 0.00000