HEADER HYDROLASE 23-MAY-14 4PNC TITLE E. COLI METHIONINE AMINOPEPTIDASE IN COMPLEX WITH INHIBITOR 7-METHOXY- TITLE 2 2-METHYLEN-3,4-DIHYDRONAPHTHALEN-1(2H)-ONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONINE AMINOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: METAP,PEPTIDASE M; COMPND 5 EC: 3.4.11.18; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: MAP, BN17_45901, BU34_07510, ECS0170, LF82_1274; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS HYDROLASE(ALPHA-AMINOACYLPEPTIDE), METAL COMPLEX, METHIONINE KEYWDS 2 AMINOPEPTIDASE, COVALENT INHIBITOR, 1-TETRALONE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.J.SCHEIDIG,M.ALTMEYER,C.D.KLEIN REVDAT 6 27-DEC-23 4PNC 1 LINK REVDAT 5 20-NOV-19 4PNC 1 REMARK LINK REVDAT 4 27-SEP-17 4PNC 1 SOURCE JRNL REMARK REVDAT 3 10-DEC-14 4PNC 1 JRNL REVDAT 2 05-NOV-14 4PNC 1 JRNL REVDAT 1 23-JUL-14 4PNC 0 JRNL AUTH M.ALTMEYER,E.AMTMANN,C.HEYL,A.MARSCHNER,A.J.SCHEIDIG, JRNL AUTH 2 C.D.KLEIN JRNL TITL BETA-AMINOKETONES AS PRODRUGS FOR SELECTIVE IRREVERSIBLE JRNL TITL 2 INHIBITORS OF TYPE-1 METHIONINE AMINOPEPTIDASES. JRNL REF BIOORG.MED.CHEM.LETT. V. 24 5310 2014 JRNL REFN ESSN 1464-3405 JRNL PMID 25293447 JRNL DOI 10.1016/J.BMCL.2014.09.047 REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 29747 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) : 0.134 REMARK 3 R VALUE (WORKING SET) : 0.132 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1566 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1854 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.1550 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.2410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2032 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 475 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : 0.78000 REMARK 3 B33 (A**2) : -0.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.41000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.080 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.023 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2259 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2205 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3078 ; 2.272 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5121 ; 0.963 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 300 ; 6.397 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 98 ;35.656 ;24.490 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 423 ;11.565 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;18.428 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 349 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2566 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 478 ; 0.002 ; 0.020 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): 1119 ; 1.300 ; 0.927 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1118 ; 1.210 ; 0.923 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1415 ; 1.955 ; 1.384 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1416 ; 1.983 ; 1.388 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1140 ; 2.511 ; 1.241 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1141 ; 2.510 ; 1.242 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1652 ; 3.810 ; 1.742 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3153 ; 6.782 ;10.999 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2830 ; 6.340 ; 9.344 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 : 1.20 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 REMARK 4 REMARK 4 4PNC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000201737. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MONTEL MIRRORS REMARK 200 OPTICS : MONTEL MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOMAR REMARK 200 DATA SCALING SOFTWARE : XDS, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61073 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02500 REMARK 200 FOR THE DATA SET : 31.0900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.01 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.11300 REMARK 200 FOR SHELL : 10.67 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, COBALT CHLORIDE, HEPES, REMARK 280 METHIONINE, SODIUM CHLORIDE, POTASSIUM CHLORIDE, PH 7.1, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 33.41000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 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 465 GLU A 264 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 OE2 GLU A 148 O HOH A 616 0.78 REMARK 500 O TYR A 168 O HOH A 832 1.29 REMARK 500 OH TYR A 62 O HOH A 401 1.43 REMARK 500 OE1 GLU A 29 O HOH A 402 1.61 REMARK 500 NH1 ARG A 19 O HOH A 874 1.66 REMARK 500 NA NA A 305 O HOH A 838 1.68 REMARK 500 O HOH A 403 O HOH A 443 1.74 REMARK 500 O HOH A 516 O HOH A 741 1.79 REMARK 500 O HOH A 516 O HOH A 607 1.83 REMARK 500 O HOH A 491 O HOH A 875 1.87 REMARK 500 O HOH A 734 O HOH A 873 1.92 REMARK 500 O HOH A 502 O HOH A 870 1.93 REMARK 500 O HOH A 695 O HOH A 856 1.94 REMARK 500 CE MET A 199 O HOH A 870 1.97 REMARK 500 ND1 HIS A 63 O HOH A 403 2.00 REMARK 500 C ASP A 263 O HOH A 405 2.02 REMARK 500 O HOH A 445 O HOH A 570 2.04 REMARK 500 CD GLU A 148 O HOH A 616 2.04 REMARK 500 CE MET A 206 O HOH A 778 2.05 REMARK 500 O HOH A 459 O HOH A 549 2.05 REMARK 500 O HOH A 818 O HOH A 841 2.06 REMARK 500 OE2 GLU A 167 O HOH A 404 2.07 REMARK 500 O HOH A 667 O HOH A 832 2.08 REMARK 500 SG CYS A 169 O HOH A 522 2.09 REMARK 500 NH2 ARG A 19 O HOH A 795 2.09 REMARK 500 O HOH A 416 O HOH A 482 2.11 REMARK 500 O HOH A 844 O HOH A 845 2.12 REMARK 500 O HOH A 585 O HOH A 857 2.13 REMARK 500 OD1 ASP A 263 O HOH A 405 2.15 REMARK 500 OE1 GLU A 167 O HOH A 406 2.16 REMARK 500 O HOH A 797 O HOH A 868 2.17 REMARK 500 CE1 HIS A 63 O HOH A 510 2.19 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 O HOH A 520 O HOH A 547 1655 1.84 REMARK 500 O HOH A 558 O HOH A 575 1655 1.87 REMARK 500 O HOH A 484 O HOH A 566 1655 1.88 REMARK 500 O HOH A 518 O HOH A 559 2645 1.90 REMARK 500 O HOH A 486 O HOH A 566 1655 1.98 REMARK 500 O HOH A 408 O HOH A 506 1655 2.03 REMARK 500 REMARK 500 REMARK: NULL 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 190 CD GLU A 190 OE2 0.068 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 19 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 19 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 19 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ASP A 90 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ASP A 90 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 MET A 121 CG - SD - CE ANGL. DEV. = 14.3 DEGREES REMARK 500 ARG A 127 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 166 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 166 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 189 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 189 NE - CZ - NH2 ANGL. DEV. = -7.1 DEGREES REMARK 500 MET A 206 CG - SD - CE ANGL. DEV. = -12.5 DEGREES REMARK 500 ASP A 253 CB - CG - OD1 ANGL. DEV. = -5.5 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 ALA A 55 -165.95 -128.57 REMARK 500 ASN A 74 -115.63 52.20 REMARK 500 GLU A 204 54.93 -151.02 REMARK 500 TRP A 221 -52.82 -123.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 803 DISTANCE = 8.06 ANGSTROMS 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 CO A 304 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 54 NE2 REMARK 620 2 GLU A 123 OE2 93.3 REMARK 620 3 HOH A 425 O 91.6 24.8 REMARK 620 4 HOH A 489 O 93.2 64.7 89.5 REMARK 620 5 HOH A 517 O 86.8 122.5 97.7 172.8 REMARK 620 6 HOH A 538 O 91.8 148.4 172.8 83.9 88.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 74 O REMARK 620 2 VAL A 76 O 88.0 REMARK 620 3 SER A 231 O 84.8 122.9 REMARK 620 4 HOH A 660 O 158.3 93.3 76.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 302 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 97 OD1 REMARK 620 2 ASP A 97 OD2 57.3 REMARK 620 3 ASP A 108 OD1 98.9 155.6 REMARK 620 4 GLU A 235 OE1 93.7 98.6 87.5 REMARK 620 5 HOH A 634 O 87.7 86.3 87.5 175.0 REMARK 620 6 HOH A 684 O 150.9 93.6 109.9 91.5 89.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 303 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 108 OD2 REMARK 620 2 HIS A 171 NE2 88.6 REMARK 620 3 GLU A 204 OE2 163.8 89.3 REMARK 620 4 GLU A 235 OE2 88.4 131.0 80.9 REMARK 620 5 HOH A 684 O 96.1 125.0 98.2 103.9 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 7NP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MAT RELATED DB: PDB REMARK 900 CO(II) FORM OF THE E. COLI METHIONINE AMINOPEPTIDASE WITHOUT LIGAND REMARK 900 RELATED ID: 1XNZ RELATED DB: PDB REMARK 900 MN(II) FORM OF THE E. COLI METHIONINE AMINOPEPTIDASE IN COMPLEX REMARK 900 WITH 5-(2-CHLOROPHENYL)FURAN-2-CARBOXYLIC ACID REMARK 900 RELATED ID: 1YVM RELATED DB: PDB REMARK 900 CO(II) FORM OF THE E. COLI METHIONINE AMINOPEPTIDASE IN COMPLEX REMARK 900 WITH THIABENDAZOLE DBREF 4PNC A 1 264 UNP C3TPN7 C3TPN7_ECOLX 1 264 SEQADV 4PNC GLN A 175 UNP C3TPN7 ARG 175 ENGINEERED MUTATION SEQRES 1 A 264 MET ALA ILE SER ILE LYS THR PRO GLU ASP ILE GLU LYS SEQRES 2 A 264 MET ARG VAL ALA GLY ARG LEU ALA ALA GLU VAL LEU GLU SEQRES 3 A 264 MET ILE GLU PRO TYR VAL LYS PRO GLY VAL SER THR GLY SEQRES 4 A 264 GLU LEU ASP ARG ILE CYS ASN ASP TYR ILE VAL ASN GLU SEQRES 5 A 264 GLN HIS ALA VAL SER ALA CYS LEU GLY TYR HIS GLY TYR SEQRES 6 A 264 PRO LYS SER VAL CYS ILE SER ILE ASN GLU VAL VAL CYS SEQRES 7 A 264 HIS GLY ILE PRO ASP ASP ALA LYS LEU LEU LYS ASP GLY SEQRES 8 A 264 ASP ILE VAL ASN ILE ASP VAL THR VAL ILE LYS ASP GLY SEQRES 9 A 264 PHE HIS GLY ASP THR SER LYS MET PHE ILE VAL GLY LYS SEQRES 10 A 264 PRO THR ILE MET GLY GLU ARG LEU CYS ARG ILE THR GLN SEQRES 11 A 264 GLU SER LEU TYR LEU ALA LEU ARG MET VAL LYS PRO GLY SEQRES 12 A 264 ILE ASN LEU ARG GLU ILE GLY ALA ALA ILE GLN LYS PHE SEQRES 13 A 264 VAL GLU ALA GLU GLY PHE SER VAL VAL ARG GLU TYR CYS SEQRES 14 A 264 GLY HIS GLY ILE GLY GLN GLY PHE HIS GLU GLU PRO GLN SEQRES 15 A 264 VAL LEU HIS TYR ASP SER ARG GLU THR ASN VAL VAL LEU SEQRES 16 A 264 LYS PRO GLY MET THR PHE THR ILE GLU PRO MET VAL ASN SEQRES 17 A 264 ALA GLY LYS LYS GLU ILE ARG THR MET LYS ASP GLY TRP SEQRES 18 A 264 THR VAL LYS THR LYS ASP ARG SER LEU SER ALA GLN TYR SEQRES 19 A 264 GLU HIS THR ILE VAL VAL THR ASP ASN GLY CYS GLU ILE SEQRES 20 A 264 LEU THR LEU ARG LYS ASP ASP THR ILE PRO ALA ILE ILE SEQRES 21 A 264 SER HIS ASP GLU HET 7NP A 301 14 HET CO A 302 1 HET CO A 303 1 HET CO A 304 1 HET NA A 305 1 HETNAM 7NP (2S)-7-METHOXY-2-METHYL-3,4-DIHYDRONAPHTHALEN-1(2H)-ONE HETNAM CO COBALT (II) ION HETNAM NA SODIUM ION HETSYN 7NP BOUND FORM OF 7-METHOXY-2-(PIPERIDIN-1-YLMETHYL)-3,4- HETSYN 2 7NP DIHYDRONAPHTHALEN-1(2H)-ONE HYDROCHLORDIDE FORMUL 2 7NP C12 H14 O2 FORMUL 3 CO 3(CO 2+) FORMUL 6 NA NA 1+ FORMUL 7 HOH *475(H2 O) HELIX 1 AA1 THR A 7 GLU A 29 1 23 HELIX 2 AA2 PRO A 30 VAL A 32 5 3 HELIX 3 AA3 SER A 37 GLU A 52 1 16 HELIX 4 AA4 GLY A 61 TYR A 65 5 5 HELIX 5 AA5 THR A 119 ARG A 138 1 20 HELIX 6 AA6 ASN A 145 GLU A 160 1 16 SHEET 1 AA1 3 VAL A 56 SER A 57 0 SHEET 2 AA1 3 ILE A 93 LYS A 102 -1 O ILE A 101 N VAL A 56 SHEET 3 AA1 3 CYS A 70 ILE A 73 -1 N SER A 72 O ASN A 95 SHEET 1 AA2 3 VAL A 56 SER A 57 0 SHEET 2 AA2 3 ILE A 93 LYS A 102 -1 O ILE A 101 N VAL A 56 SHEET 3 AA2 3 PHE A 105 ILE A 114 -1 O THR A 109 N VAL A 98 SHEET 1 AA3 3 VAL A 76 CYS A 78 0 SHEET 2 AA3 3 VAL A 223 THR A 225 -1 O VAL A 223 N VAL A 77 SHEET 3 AA3 3 ILE A 214 THR A 216 -1 N ARG A 215 O LYS A 224 SHEET 1 AA4 3 SER A 163 VAL A 164 0 SHEET 2 AA4 3 MET A 206 ASN A 208 -1 O ASN A 208 N SER A 163 SHEET 3 AA4 3 SER A 231 GLN A 233 -1 O ALA A 232 N VAL A 207 SHEET 1 AA5 2 GLY A 170 GLY A 172 0 SHEET 2 AA5 2 GLU A 179 VAL A 183 -1 O GLU A 179 N GLY A 172 SHEET 1 AA6 4 THR A 200 ILE A 203 0 SHEET 2 AA6 4 HIS A 236 THR A 241 -1 O ILE A 238 N PHE A 201 SHEET 3 AA6 4 GLY A 244 ILE A 247 -1 O GLU A 246 N VAL A 239 SHEET 4 AA6 4 ILE A 259 SER A 261 -1 O ILE A 260 N CYS A 245 LINK SG ACYS A 59 CAN 7NP A 301 1555 1555 1.95 LINK SG BCYS A 59 CAN 7NP A 301 1555 1555 1.81 LINK NE2 HIS A 54 CO CO A 304 1555 1555 2.22 LINK O ASN A 74 NA NA A 305 1555 1555 2.56 LINK O VAL A 76 NA NA A 305 1555 1555 2.43 LINK OD1 ASP A 97 CO CO A 302 1555 1555 2.07 LINK OD2 ASP A 97 CO CO A 302 1555 1555 2.41 LINK OD1 ASP A 108 CO CO A 302 1555 1555 2.00 LINK OD2 ASP A 108 CO CO A 303 1555 1555 2.10 LINK OE2 GLU A 123 CO CO A 304 1555 2656 2.27 LINK NE2 HIS A 171 CO CO A 303 1555 1555 2.05 LINK OE2 GLU A 204 CO CO A 303 1555 1555 2.17 LINK O SER A 231 NA NA A 305 1555 1555 2.43 LINK OE1 GLU A 235 CO CO A 302 1555 1555 2.16 LINK OE2 GLU A 235 CO CO A 303 1555 1555 1.97 LINK CO CO A 302 O HOH A 634 1555 1555 2.25 LINK CO CO A 302 O HOH A 684 1555 1555 2.01 LINK CO CO A 303 O HOH A 684 1555 1555 1.98 LINK CO CO A 304 O HOH A 425 1555 1555 2.13 LINK CO CO A 304 O HOH A 489 1555 1555 2.18 LINK CO CO A 304 O HOH A 517 1555 1555 2.03 LINK CO CO A 304 O HOH A 538 1555 1555 2.00 LINK NA NA A 305 O HOH A 660 1555 1555 3.12 CISPEP 1 GLU A 180 PRO A 181 0 0.08 SITE 1 AC1 10 CYS A 59 TYR A 62 TYR A 65 CYS A 70 SITE 2 AC1 10 HIS A 79 PHE A 177 HIS A 178 TRP A 221 SITE 3 AC1 10 HOH A 628 HOH A 873 SITE 1 AC2 6 ASP A 97 ASP A 108 GLU A 235 CO A 303 SITE 2 AC2 6 HOH A 634 HOH A 684 SITE 1 AC3 7 ASP A 108 HIS A 171 THR A 202 GLU A 204 SITE 2 AC3 7 GLU A 235 CO A 302 HOH A 684 SITE 1 AC4 5 HIS A 54 HOH A 425 HOH A 489 HOH A 517 SITE 2 AC4 5 HOH A 538 SITE 1 AC5 5 SER A 72 ASN A 74 VAL A 76 SER A 231 SITE 2 AC5 5 HOH A 838 CRYST1 39.010 66.820 48.450 90.00 111.15 90.00 P 1 21 1 2 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 0.025634 0.000000 0.009918 0.00000 SCALE2 0.000000 0.014966 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022131 0.00000