HEADER HYDROLASE 01-JUN-04 1WKM TITLE THE PRODUCT BOUND FORM OF THE MN(II)LOADED METHIONINE AMINOPEPTIDASE TITLE 2 FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONINE AMINOPEPTIDASE; COMPND 3 CHAIN: A, B; 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: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMINOPEPTIDASE, HYPERTHERMOPHILE, METHIONINE COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.J.COPIK,B.P.NOCEK,S.B.JANG,S.I.SWIERCZEK,S.RUEBUSH,L.MENG, AUTHOR 2 V.M.D'SOUZA,J.W.PETERS,B.BENNETT,R.C.HOLZ REVDAT 3 25-OCT-23 1WKM 1 REMARK LINK REVDAT 2 24-FEB-09 1WKM 1 VERSN REVDAT 1 22-FEB-05 1WKM 0 JRNL AUTH A.J.COPIK,B.P.NOCEK,S.I.SWIERCZEK,S.RUEBUSH,S.B.JANG,L.MENG, JRNL AUTH 2 V.M.D'SOUZA,J.W.PETERS,B.BENNETT,R.C.HOLZ JRNL TITL EPR AND X-RAY CRYSTALLOGRAPHIC CHARACTERIZATION OF THE JRNL TITL 2 PRODUCT-BOUND FORM OF THE MNII-LOADED METHIONYL JRNL TITL 3 AMINOPEPTIDASE FROM PYROCOCCUS FURIOSUS JRNL REF BIOCHEMISTRY V. 44 121 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15628852 JRNL DOI 10.1021/BI048123+ REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1784938.560 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 38795 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 SET) : 0.215 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1956 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6120 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 328 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4624 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 325 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.66000 REMARK 3 B22 (A**2) : -2.66000 REMARK 3 B33 (A**2) : 5.31000 REMARK 3 B12 (A**2) : 2.79000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.17 REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 2.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.900 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.280 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.990 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.100 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.050 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 35.15 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : PATCH-NEW.PARAM REMARK 3 PARAMETER FILE 3 : MTE.PARAM REMARK 3 PARAMETER FILE 4 : WATER.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : PATCH-NEW.TOP REMARK 3 TOPOLOGY FILE 3 : MTE.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WKM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000023679. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL 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: AMORE REMARK 200 STARTING MODEL: 1XGM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% ETHANOL, TRIS , PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 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 REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 40.98667 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 81.97333 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 0.00000 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 40.98667 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 81.97333 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 MET A 1 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 MET A 7 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 17 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 25 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 MET A 28 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 MET A 40 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 MET A 42 CG - SD - CE ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 99 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 MET A 102 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 MET A 108 CG - SD - CE ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 123 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 140 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 142 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 157 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 171 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 MET A 207 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 210 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 215 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 220 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 228 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 238 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 MET A 244 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 272 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 GLU A 295 CA - C - O ANGL. DEV. = -13.1 DEGREES REMARK 500 ARG B 17 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 25 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 MET B 28 CG - SD - CE ANGL. DEV. = 9.6 DEGREES REMARK 500 MET B 40 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 MET B 42 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG B 99 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 MET B 102 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 MET B 108 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG B 123 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 140 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 142 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 157 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 171 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 MET B 207 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG B 210 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 215 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 220 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 228 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 238 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 MET B 244 CG - SD - CE ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG B 272 NE - CZ - NH2 ANGL. DEV. = 3.7 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 57 -131.62 45.27 REMARK 500 HIS A 62 38.19 71.33 REMARK 500 VAL A 209 -41.42 -138.12 REMARK 500 SER A 289 -179.98 -171.80 REMARK 500 ASN B 57 -129.93 45.05 REMARK 500 HIS B 62 36.99 70.16 REMARK 500 VAL B 209 -22.30 -141.81 REMARK 500 ARG B 210 136.65 -173.09 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 297 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 82 OD1 REMARK 620 2 ASP A 82 OD2 65.4 REMARK 620 3 ASP A 93 OD1 149.9 86.7 REMARK 620 4 GLU A 280 OE1 89.4 98.6 83.8 REMARK 620 5 MET A1298 N 83.9 92.0 109.2 163.8 REMARK 620 6 MET A1298 OXT 107.7 157.7 102.4 102.5 65.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 296 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 93 OD2 REMARK 620 2 HIS A 153 NE2 100.2 REMARK 620 3 GLU A 187 OE2 170.3 81.5 REMARK 620 4 GLU A 280 OE2 85.2 129.6 86.4 REMARK 620 5 MET A1298 OXT 93.4 108.6 95.1 121.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 296 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 82 OD1 REMARK 620 2 ASP B 82 OD2 66.9 REMARK 620 3 ASP B 93 OD1 153.8 87.1 REMARK 620 4 GLU B 280 OE1 101.0 92.3 82.2 REMARK 620 5 MET B2298 N 69.2 96.7 113.1 162.5 REMARK 620 6 MET B2298 OXT 100.5 162.7 104.2 102.1 66.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 297 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 93 OD2 REMARK 620 2 HIS B 153 NE2 100.2 REMARK 620 3 GLU B 187 OE2 171.6 79.6 REMARK 620 4 GLU B 280 OE2 85.1 131.5 88.8 REMARK 620 5 MET B2298 OXT 93.2 108.4 94.8 119.4 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 MN A 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 297 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 297 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MET A 1298 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MET B 2298 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XGM RELATED DB: PDB REMARK 900 RELATED ID: 1XGN RELATED DB: PDB DBREF 1WKM A 1 295 UNP P56218 AMPM_PYRFU 1 295 DBREF 1WKM B 1 295 UNP P56218 AMPM_PYRFU 1 295 SEQRES 1 A 295 MET ASP THR GLU LYS LEU MET LYS ALA GLY GLU ILE ALA SEQRES 2 A 295 LYS LYS VAL ARG GLU LYS ALA ILE LYS LEU ALA ARG PRO SEQRES 3 A 295 GLY MET LEU LEU LEU GLU LEU ALA GLU SER ILE GLU LYS SEQRES 4 A 295 MET ILE MET GLU LEU GLY GLY LYS PRO ALA PHE PRO VAL SEQRES 5 A 295 ASN LEU SER ILE ASN GLU ILE ALA ALA HIS TYR THR PRO SEQRES 6 A 295 TYR LYS GLY ASP THR THR VAL LEU LYS GLU GLY ASP TYR SEQRES 7 A 295 LEU LYS ILE ASP VAL GLY VAL HIS ILE ASP GLY PHE ILE SEQRES 8 A 295 ALA ASP THR ALA VAL THR VAL ARG VAL GLY MET GLU GLU SEQRES 9 A 295 ASP GLU LEU MET GLU ALA ALA LYS GLU ALA LEU ASN ALA SEQRES 10 A 295 ALA ILE SER VAL ALA ARG ALA GLY VAL GLU ILE LYS GLU SEQRES 11 A 295 LEU GLY LYS ALA ILE GLU ASN GLU ILE ARG LYS ARG GLY SEQRES 12 A 295 PHE LYS PRO ILE VAL ASN LEU SER GLY HIS LYS ILE GLU SEQRES 13 A 295 ARG TYR LYS LEU HIS ALA GLY ILE SER ILE PRO ASN ILE SEQRES 14 A 295 TYR ARG PRO HIS ASP ASN TYR VAL LEU LYS GLU GLY ASP SEQRES 15 A 295 VAL PHE ALA ILE GLU PRO PHE ALA THR ILE GLY ALA GLY SEQRES 16 A 295 GLN VAL ILE GLU VAL PRO PRO THR LEU ILE TYR MET TYR SEQRES 17 A 295 VAL ARG ASP VAL PRO VAL ARG VAL ALA GLN ALA ARG PHE SEQRES 18 A 295 LEU LEU ALA LYS ILE LYS ARG GLU TYR GLY THR LEU PRO SEQRES 19 A 295 PHE ALA TYR ARG TRP LEU GLN ASN ASP MET PRO GLU GLY SEQRES 20 A 295 GLN LEU LYS LEU ALA LEU LYS THR LEU GLU LYS ALA GLY SEQRES 21 A 295 ALA ILE TYR GLY TYR PRO VAL LEU LYS GLU ILE ARG ASN SEQRES 22 A 295 GLY ILE VAL ALA GLN PHE GLU HIS THR ILE ILE VAL GLU SEQRES 23 A 295 LYS ASP SER VAL ILE VAL THR THR GLU SEQRES 1 B 295 MET ASP THR GLU LYS LEU MET LYS ALA GLY GLU ILE ALA SEQRES 2 B 295 LYS LYS VAL ARG GLU LYS ALA ILE LYS LEU ALA ARG PRO SEQRES 3 B 295 GLY MET LEU LEU LEU GLU LEU ALA GLU SER ILE GLU LYS SEQRES 4 B 295 MET ILE MET GLU LEU GLY GLY LYS PRO ALA PHE PRO VAL SEQRES 5 B 295 ASN LEU SER ILE ASN GLU ILE ALA ALA HIS TYR THR PRO SEQRES 6 B 295 TYR LYS GLY ASP THR THR VAL LEU LYS GLU GLY ASP TYR SEQRES 7 B 295 LEU LYS ILE ASP VAL GLY VAL HIS ILE ASP GLY PHE ILE SEQRES 8 B 295 ALA ASP THR ALA VAL THR VAL ARG VAL GLY MET GLU GLU SEQRES 9 B 295 ASP GLU LEU MET GLU ALA ALA LYS GLU ALA LEU ASN ALA SEQRES 10 B 295 ALA ILE SER VAL ALA ARG ALA GLY VAL GLU ILE LYS GLU SEQRES 11 B 295 LEU GLY LYS ALA ILE GLU ASN GLU ILE ARG LYS ARG GLY SEQRES 12 B 295 PHE LYS PRO ILE VAL ASN LEU SER GLY HIS LYS ILE GLU SEQRES 13 B 295 ARG TYR LYS LEU HIS ALA GLY ILE SER ILE PRO ASN ILE SEQRES 14 B 295 TYR ARG PRO HIS ASP ASN TYR VAL LEU LYS GLU GLY ASP SEQRES 15 B 295 VAL PHE ALA ILE GLU PRO PHE ALA THR ILE GLY ALA GLY SEQRES 16 B 295 GLN VAL ILE GLU VAL PRO PRO THR LEU ILE TYR MET TYR SEQRES 17 B 295 VAL ARG ASP VAL PRO VAL ARG VAL ALA GLN ALA ARG PHE SEQRES 18 B 295 LEU LEU ALA LYS ILE LYS ARG GLU TYR GLY THR LEU PRO SEQRES 19 B 295 PHE ALA TYR ARG TRP LEU GLN ASN ASP MET PRO GLU GLY SEQRES 20 B 295 GLN LEU LYS LEU ALA LEU LYS THR LEU GLU LYS ALA GLY SEQRES 21 B 295 ALA ILE TYR GLY TYR PRO VAL LEU LYS GLU ILE ARG ASN SEQRES 22 B 295 GLY ILE VAL ALA GLN PHE GLU HIS THR ILE ILE VAL GLU SEQRES 23 B 295 LYS ASP SER VAL ILE VAL THR THR GLU HET MN A 296 1 HET MN A 297 1 HET MET A1298 9 HET MN B 296 1 HET MN B 297 1 HET MET B2298 9 HETNAM MN MANGANESE (II) ION HETNAM MET METHIONINE FORMUL 3 MN 4(MN 2+) FORMUL 5 MET 2(C5 H11 N O2 S) FORMUL 9 HOH *325(H2 O) HELIX 1 1 ASP A 2 ALA A 24 1 23 HELIX 2 2 LEU A 29 LEU A 44 1 16 HELIX 3 3 ASP A 105 ALA A 122 1 18 HELIX 4 4 ILE A 128 LYS A 141 1 14 HELIX 5 5 VAL A 216 GLY A 231 1 16 HELIX 6 6 ARG A 238 GLN A 241 5 4 HELIX 7 7 PRO A 245 ALA A 259 1 15 HELIX 8 8 ASP B 2 ALA B 24 1 23 HELIX 9 9 LEU B 29 LEU B 44 1 16 HELIX 10 10 ASP B 105 ALA B 122 1 18 HELIX 11 11 GLU B 127 LYS B 141 1 15 HELIX 12 12 VAL B 216 GLY B 231 1 16 HELIX 13 13 ARG B 238 GLN B 241 5 4 HELIX 14 14 PRO B 245 ALA B 259 1 15 SHEET 1 A 3 LYS A 47 PRO A 48 0 SHEET 2 A 3 TYR A 78 ILE A 87 -1 O HIS A 86 N LYS A 47 SHEET 3 A 3 ASN A 53 ILE A 56 -1 N SER A 55 O LYS A 80 SHEET 1 B 3 LYS A 47 PRO A 48 0 SHEET 2 B 3 TYR A 78 ILE A 87 -1 O HIS A 86 N LYS A 47 SHEET 3 B 3 PHE A 90 ARG A 99 -1 O VAL A 98 N LEU A 79 SHEET 1 C 4 ILE A 59 ALA A 61 0 SHEET 2 C 4 ILE A 262 GLU A 270 -1 O LEU A 268 N ALA A 61 SHEET 3 C 4 VAL A 197 TYR A 208 -1 N ILE A 205 O TYR A 265 SHEET 4 C 4 PHE A 235 ALA A 236 -1 O PHE A 235 N TYR A 206 SHEET 1 D 3 LYS A 145 PRO A 146 0 SHEET 2 D 3 PHE A 189 THR A 191 -1 O THR A 191 N LYS A 145 SHEET 3 D 3 VAL A 276 GLN A 278 -1 O ALA A 277 N ALA A 190 SHEET 1 E 5 SER A 165 ILE A 166 0 SHEET 2 E 5 GLY A 152 LYS A 154 -1 N GLY A 152 O ILE A 166 SHEET 3 E 5 VAL A 183 ILE A 186 -1 O ALA A 185 N HIS A 153 SHEET 4 E 5 HIS A 281 VAL A 285 -1 O ILE A 283 N PHE A 184 SHEET 5 E 5 VAL A 290 VAL A 292 -1 O ILE A 291 N ILE A 284 SHEET 1 F 3 LYS B 47 PRO B 48 0 SHEET 2 F 3 TYR B 78 ILE B 87 -1 O HIS B 86 N LYS B 47 SHEET 3 F 3 ASN B 53 ILE B 56 -1 N SER B 55 O LYS B 80 SHEET 1 G 3 LYS B 47 PRO B 48 0 SHEET 2 G 3 TYR B 78 ILE B 87 -1 O HIS B 86 N LYS B 47 SHEET 3 G 3 PHE B 90 ARG B 99 -1 O VAL B 96 N ILE B 81 SHEET 1 H 4 ILE B 59 ALA B 61 0 SHEET 2 H 4 ILE B 262 GLU B 270 -1 O LEU B 268 N ALA B 61 SHEET 3 H 4 VAL B 197 TYR B 208 -1 N ILE B 205 O TYR B 265 SHEET 4 H 4 PHE B 235 ALA B 236 -1 O PHE B 235 N TYR B 206 SHEET 1 I 3 LYS B 145 PRO B 146 0 SHEET 2 I 3 PHE B 189 THR B 191 -1 O THR B 191 N LYS B 145 SHEET 3 I 3 VAL B 276 GLN B 278 -1 O ALA B 277 N ALA B 190 SHEET 1 J 5 SER B 165 ILE B 166 0 SHEET 2 J 5 GLY B 152 LYS B 154 -1 N GLY B 152 O ILE B 166 SHEET 3 J 5 VAL B 183 ILE B 186 -1 O ALA B 185 N HIS B 153 SHEET 4 J 5 HIS B 281 VAL B 285 -1 O ILE B 283 N PHE B 184 SHEET 5 J 5 VAL B 290 VAL B 292 -1 O ILE B 291 N ILE B 284 LINK OD1 ASP A 82 MN MN A 297 1555 1555 2.13 LINK OD2 ASP A 82 MN MN A 297 1555 1555 2.01 LINK OD2 ASP A 93 MN MN A 296 1555 1555 1.94 LINK OD1 ASP A 93 MN MN A 297 1555 1555 2.05 LINK NE2 HIS A 153 MN MN A 296 1555 1555 2.13 LINK OE2 GLU A 187 MN MN A 296 1555 1555 2.12 LINK OE2 GLU A 280 MN MN A 296 1555 1555 1.99 LINK OE1 GLU A 280 MN MN A 297 1555 1555 2.00 LINK MN MN A 296 OXT MET A1298 1555 1555 1.91 LINK MN MN A 297 N MET A1298 1555 1555 2.09 LINK MN MN A 297 OXT MET A1298 1555 1555 2.71 LINK OD1 ASP B 82 MN MN B 296 1555 1555 2.07 LINK OD2 ASP B 82 MN MN B 296 1555 1555 1.98 LINK OD1 ASP B 93 MN MN B 296 1555 1555 2.06 LINK OD2 ASP B 93 MN MN B 297 1555 1555 1.98 LINK NE2 HIS B 153 MN MN B 297 1555 1555 2.14 LINK OE2 GLU B 187 MN MN B 297 1555 1555 2.03 LINK OE1 GLU B 280 MN MN B 296 1555 1555 2.01 LINK OE2 GLU B 280 MN MN B 297 1555 1555 1.98 LINK MN MN B 296 N MET B2298 1555 1555 2.12 LINK MN MN B 296 OXT MET B2298 1555 1555 2.72 LINK MN MN B 297 OXT MET B2298 1555 1555 1.91 CISPEP 1 PRO A 201 PRO A 202 0 0.69 CISPEP 2 PRO B 201 PRO B 202 0 0.70 SITE 1 AC1 6 ASP A 93 HIS A 153 GLU A 187 GLU A 280 SITE 2 AC1 6 MN A 297 MET A1298 SITE 1 AC2 5 ASP A 82 ASP A 93 GLU A 280 MN A 296 SITE 2 AC2 5 MET A1298 SITE 1 AC3 5 ASP B 82 ASP B 93 GLU B 280 MN B 297 SITE 2 AC3 5 MET B2298 SITE 1 AC4 6 ASP B 93 HIS B 153 GLU B 187 GLU B 280 SITE 2 AC4 6 MN B 296 MET B2298 SITE 1 AC5 12 PHE A 50 ASN A 53 HIS A 62 ASP A 82 SITE 2 AC5 12 ASP A 93 HIS A 153 HIS A 161 GLU A 187 SITE 3 AC5 12 ILE A 205 GLU A 280 MN A 296 MN A 297 SITE 1 AC6 12 PHE B 50 ASN B 53 HIS B 62 ASP B 82 SITE 2 AC6 12 ASP B 93 HIS B 153 HIS B 161 GLU B 187 SITE 3 AC6 12 ILE B 205 GLU B 280 MN B 296 MN B 297 CRYST1 112.010 112.010 122.960 90.00 90.00 120.00 P 64 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 0.008928 0.005154 0.000000 0.00000 SCALE2 0.000000 0.010309 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008133 0.00000