HEADER OXIDOREDUCTASE 19-JAN-11 2Y60 TITLE ISOPENICILLIN N SYNTHASE WITH AC-D-METHIONINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOPENICILLIN N SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IPNS; COMPND 5 EC: 1.21.3.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EMERICELLA NIDULANS; SOURCE 3 ORGANISM_TAXID: 162425; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: NM554; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PJB703 KEYWDS OXIDOREDUCTASE, OXYGENASE, PENICILLIN BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR P.J.RUTLEDGE,I.J.CLIFTON,W.GE REVDAT 4 20-DEC-23 2Y60 1 REMARK LINK REVDAT 3 17-JUL-19 2Y60 1 REMARK REVDAT 2 15-AUG-12 2Y60 1 JRNL REMARK HETSYN REVDAT 1 08-FEB-12 2Y60 0 JRNL AUTH I.J.CLIFTON,W.GE,R.M.ADLINGTON,J.E.BALDWIN,P.J.RUTLEDGE JRNL TITL THE CRYSTAL STRUCTURE OF ISOPENICILLIN N SYNTHASE WITH JRNL TITL 2 DELTA((L)-ALPHA-AMINOADIPOYL)-(L)-CYSTEINYL-(D)-METHIONINE JRNL TITL 3 REVEALS THIOETHER COORDINATION TO IRON. JRNL REF ARCH.BIOCHEM.BIOPHYS. V. 516 103 2011 JRNL REFN ISSN 0003-9861 JRNL PMID 22001738 JRNL DOI 10.1016/J.ABB.2011.09.014 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 83.2 REMARK 3 NUMBER OF REFLECTIONS : 53070 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) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2213 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3869 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 143 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2639 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 392 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.41000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : -0.39000 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): 0.074 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.036 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.787 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2768 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3767 ; 2.068 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 332 ; 6.288 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 142 ;34.011 ;24.718 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 432 ;12.216 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;14.961 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 392 ; 0.146 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2178 ; 0.013 ; 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): 1652 ; 2.602 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2673 ; 3.700 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1116 ; 5.439 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1092 ; 7.445 ; 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): 2755 ; 2.875 ; 3.000 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 2Y60 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1290047029. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-98 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 : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8345 REMARK 200 MONOCHROMATOR : SI(1 1 1) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55964 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.8 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 1BK0 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M LITHIUM SULPHATE, 76MM TRIS/HCL, REMARK 280 PH 8.5, 2.0MM FERROUS SULPHATE, 2.6MG/ML TRIPEPTIDE, 25MG/ML IPNS REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 23.26150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.46150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.44100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.46150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.26150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.44100 REMARK 290 SMTRY3 4 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 GLY A 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ALA A 237 CB REMARK 470 LYS A 305 CG CD CE NZ 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 O HOH A 2392 O HOH A 2394 1.37 REMARK 500 O HOH A 2206 O HOH A 2213 1.39 REMARK 500 O HOH A 2250 O HOH A 2251 1.42 REMARK 500 O PRO A 299 O HOH A 2355 1.85 REMARK 500 O HOH A 2238 O HOH A 2351 2.00 REMARK 500 C6 M8F A 1332 O HOH A 2394 2.01 REMARK 500 OD1 ASP A 131 O HOH A 2184 2.02 REMARK 500 OG SER A 55 O HOH A 2084 2.08 REMARK 500 O HOH A 2096 O HOH A 2195 2.09 REMARK 500 O HOH A 2081 O HOH A 2212 2.11 REMARK 500 O HOH A 2275 O HOH A 2379 2.12 REMARK 500 O4 SO4 A 1334 O HOH A 2395 2.15 REMARK 500 O HOH A 2027 O HOH A 2235 2.18 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 NZ LYS A 80 O4 SO4 A 1334 2565 2.12 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 68 CD GLU A 68 OE2 -0.072 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 ASP A 131 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 173 CG - CD - NE ANGL. DEV. = -16.6 DEGREES REMARK 500 ARG A 173 CD - NE - CZ ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG A 173 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ASP A 291 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 300 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 300 NE - CZ - NH2 ANGL. DEV. = -4.1 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 ASP A 38 -109.09 -100.47 REMARK 500 HIS A 82 63.93 -103.34 REMARK 500 LYS A 97 -46.35 -136.45 REMARK 500 THR A 123 -1.60 75.33 REMARK 500 ASP A 179 -2.52 -140.16 REMARK 500 ASN A 230 -25.01 -153.33 REMARK 500 LEU A 288 -158.88 -89.73 REMARK 500 ASP A 307 38.09 -98.68 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 A2057 DISTANCE = 5.95 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 FE A1333 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 214 NE2 REMARK 620 2 ASP A 216 OD1 97.3 REMARK 620 3 HIS A 270 NE2 84.9 86.6 REMARK 620 4 M8F A1332 S13 93.0 86.1 172.1 REMARK 620 5 M8F A1332 S20 93.3 167.8 100.3 87.4 REMARK 620 6 HOH A2281 O 172.0 86.9 88.6 94.1 83.2 REMARK 620 N 1 2 3 4 5 REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: N-[(5S)-5-AMINO-5-CARBOXYPENTANOYL]-L-CYSTEINYL-D- REMARK 630 METHIONINE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 M8F A 1332 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: UN1 CYS MED REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE M8F A 1332 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 1333 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1334 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1335 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1336 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HB4 RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN EXPOSED REMARK 900 PRODUCT FROM ANAEROBIC ACOV FE COMPLEX) REMARK 900 RELATED ID: 1BLZ RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACV- FE-NO REMARK 900 COMPLEX) REMARK 900 RELATED ID: 1OC1 RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL- AMINOBUTYRATE-FE REMARK 900 COMPLEX REMARK 900 RELATED ID: 2WO7 RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE WITH SUBSTRATE ANALOGUE L,L,D -ACD2AB REMARK 900 (UNEXPOSED) REMARK 900 RELATED ID: 1W3V RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE D-(L-A-AMINOADIPOYL)-(3R)- METHYL-L- REMARK 900 CYSTEINE D-A-HYDROXYISOVALERYL ESTER COMPLEX ( ANAEROBIC) REMARK 900 RELATED ID: 1UZW RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE WITH L-D-(A-AMINOADIPOYL)-L- CYSTEINYL-D- REMARK 900 ISODEHYDROVALINE REMARK 900 RELATED ID: 1IPS RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS ( MANGANESE REMARK 900 COMPLEX) REMARK 900 RELATED ID: 1BK0 RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACV- FE COMPLEX) REMARK 900 RELATED ID: 1W3X RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE D-(L-A-AMINOADIPOYL)-(3R)- METHYL-L- REMARK 900 CYSTEINE D-A-HYDROXYISOVALERYL ESTER COMPLEX ( OXYGEN EXPOSED 5 REMARK 900 MINUTES 20 BAR) REMARK 900 RELATED ID: 2VBP RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE WITH SUBSTRATE ANALOGUE L,L,L -ACAB REMARK 900 (UNEXPOSED) REMARK 900 RELATED ID: 1W04 RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL-GLYCINE-FE -NO REMARK 900 COMPLEX REMARK 900 RELATED ID: 1HB3 RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN EXPOSED REMARK 900 PRODUCT FROM ANAEROBIC ACOV FE COMPLEX) REMARK 900 RELATED ID: 1QIQ RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACMC FE COMPLEX) REMARK 900 RELATED ID: 1QJF RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS ( MONOCYCLIC REMARK 900 SULFOXIDE - FE COMPLEX) REMARK 900 RELATED ID: 1OBN RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL- AMINOBUTYRATE-FE- REMARK 900 NO COMPLEX REMARK 900 RELATED ID: 2BU9 RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE COMPLEXED WITH L-AMINOADIPOYL-L -CYSTEINYL- REMARK 900 L-HEXAFLUOROVALINE REMARK 900 RELATED ID: 1ODM RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS ( ANAEROBIC AC- REMARK 900 VINYLGLYCINE FE COMPLEX) REMARK 900 RELATED ID: 2VBD RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE WITH SUBSTRATE ANALOGUE L,L,L -ACOMP REMARK 900 (UNEXPOSED) REMARK 900 RELATED ID: 2VCM RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE WITH SUBSTRATE ANALOGUE ASMCOV REMARK 900 RELATED ID: 1ODN RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN -EXPOSED REMARK 900 PRODUCT FROM ANAEROBIC AC-VINYLGLYCINE FE COMPLEX) REMARK 900 RELATED ID: 2VE1 RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE WITH SUBSTRATE ANALOGUE ASMCOV ( OXYGEN REMARK 900 EXPOSED 1MIN 20BAR) REMARK 900 RELATED ID: 2VAU RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE WITH SUBSTRATE ANALOGUE ACOMP ( UNEXPOSED) REMARK 900 RELATED ID: 1QJE RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (IPN - FE REMARK 900 COMPLEX) REMARK 900 RELATED ID: 1HB2 RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN EXPOSED REMARK 900 PRODUCT FROM ANAEROBIC ACOV FE COMPLEX) REMARK 900 RELATED ID: 1W03 RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL-GLYCINE-FE COMPLEX REMARK 900 RELATED ID: 2VBB RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE WITH SUBSTRATE ANALOGUE ACOMP ( 35MINUTES REMARK 900 OXYGEN EXPOSURE) REMARK 900 RELATED ID: 1W06 RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL-ALANINE-FE NO REMARK 900 COMPLEX REMARK 900 RELATED ID: 2IVJ RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS ( ANAEROBIC AC- REMARK 900 CYCLOPROPYLGLYCINE FE COMPLEX) REMARK 900 RELATED ID: 1HB1 RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS ( ANAEROBIC ACOV REMARK 900 FE COMPLEX) REMARK 900 RELATED ID: 2JB4 RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE WITH A 2-THIABICYCLOHEPTAN-6- ONE PRODUCT REMARK 900 ANALOGUE REMARK 900 RELATED ID: 1W05 RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL-ALANINE-FE COMPLEX REMARK 900 RELATED ID: 2IVI RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS ( ANAEROBIC AC- REMARK 900 METHYL-CYCLOPROPYLGLYCINE FE COMPLEX) REMARK 900 RELATED ID: 2BJS RELATED DB: PDB REMARK 900 ISOPENICILLIN N SYNTHASE C-TERMINAL TRUNCATION MUTANT DBREF 2Y60 A 1 331 UNP P05326 IPNS_EMENI 1 331 SEQRES 1 A 331 MET GLY SER VAL SER LYS ALA ASN VAL PRO LYS ILE ASP SEQRES 2 A 331 VAL SER PRO LEU PHE GLY ASP ASP GLN ALA ALA LYS MET SEQRES 3 A 331 ARG VAL ALA GLN GLN ILE ASP ALA ALA SER ARG ASP THR SEQRES 4 A 331 GLY PHE PHE TYR ALA VAL ASN HIS GLY ILE ASN VAL GLN SEQRES 5 A 331 ARG LEU SER GLN LYS THR LYS GLU PHE HIS MET SER ILE SEQRES 6 A 331 THR PRO GLU GLU LYS TRP ASP LEU ALA ILE ARG ALA TYR SEQRES 7 A 331 ASN LYS GLU HIS GLN ASP GLN VAL ARG ALA GLY TYR TYR SEQRES 8 A 331 LEU SER ILE PRO GLY LYS LYS ALA VAL GLU SER PHE CYS SEQRES 9 A 331 TYR LEU ASN PRO ASN PHE THR PRO ASP HIS PRO ARG ILE SEQRES 10 A 331 GLN ALA LYS THR PRO THR HIS GLU VAL ASN VAL TRP PRO SEQRES 11 A 331 ASP GLU THR LYS HIS PRO GLY PHE GLN ASP PHE ALA GLU SEQRES 12 A 331 GLN TYR TYR TRP ASP VAL PHE GLY LEU SER SER ALA LEU SEQRES 13 A 331 LEU LYS GLY TYR ALA LEU ALA LEU GLY LYS GLU GLU ASN SEQRES 14 A 331 PHE PHE ALA ARG HIS PHE LYS PRO ASP ASP THR LEU ALA SEQRES 15 A 331 SER VAL VAL LEU ILE ARG TYR PRO TYR LEU ASP PRO TYR SEQRES 16 A 331 PRO GLU ALA ALA ILE LYS THR ALA ALA ASP GLY THR LYS SEQRES 17 A 331 LEU SER PHE GLU TRP HIS GLU ASP VAL SER LEU ILE THR SEQRES 18 A 331 VAL LEU TYR GLN SER ASN VAL GLN ASN LEU GLN VAL GLU SEQRES 19 A 331 THR ALA ALA GLY TYR GLN ASP ILE GLU ALA ASP ASP THR SEQRES 20 A 331 GLY TYR LEU ILE ASN CYS GLY SER TYR MET ALA HIS LEU SEQRES 21 A 331 THR ASN ASN TYR TYR LYS ALA PRO ILE HIS ARG VAL LYS SEQRES 22 A 331 TRP VAL ASN ALA GLU ARG GLN SER LEU PRO PHE PHE VAL SEQRES 23 A 331 ASN LEU GLY TYR ASP SER VAL ILE ASP PRO PHE ASP PRO SEQRES 24 A 331 ARG GLU PRO ASN GLY LYS SER ASP ARG GLU PRO LEU SER SEQRES 25 A 331 TYR GLY ASP TYR LEU GLN ASN GLY LEU VAL SER LEU ILE SEQRES 26 A 331 ASN LYS ASN GLY GLN THR HET M8F A1332 25 HET FE A1333 1 HET SO4 A1334 5 HET SO4 A1335 5 HET GOL A1336 6 HETNAM M8F N-[(5S)-5-AMINO-5-CARBOXYPENTANOYL]-L-CYSTEINYL-D- HETNAM 2 M8F METHIONINE HETNAM FE FE (III) ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN M8F L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-METHIONINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 M8F C14 H25 N3 O6 S2 FORMUL 3 FE FE 3+ FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *392(H2 O) HELIX 1 1 SER A 15 GLY A 19 5 5 HELIX 2 2 ASP A 21 ASP A 38 1 18 HELIX 3 3 ASN A 50 ILE A 65 1 16 HELIX 4 4 THR A 66 ALA A 74 1 9 HELIX 5 5 HIS A 114 ALA A 119 1 6 HELIX 6 6 GLY A 137 LEU A 164 1 28 HELIX 7 7 PHE A 171 PHE A 175 5 5 HELIX 8 8 PRO A 196 ILE A 200 5 5 HELIX 9 9 GLY A 254 THR A 261 1 8 HELIX 10 10 SER A 312 GLY A 329 1 18 SHEET 1 AA 8 LYS A 11 ASP A 13 0 SHEET 2 AA 8 PHE A 41 VAL A 45 1 O TYR A 43 N ILE A 12 SHEET 3 AA 8 TYR A 249 CYS A 253 -1 O TYR A 249 N ALA A 44 SHEET 4 AA 8 ILE A 220 GLN A 225 -1 O THR A 221 N ASN A 252 SHEET 5 AA 8 ARG A 279 VAL A 286 -1 O LEU A 282 N TYR A 224 SHEET 6 AA 8 SER A 183 TYR A 189 -1 O SER A 183 N PHE A 285 SHEET 7 AA 8 GLU A 101 TYR A 105 -1 O GLU A 101 N ARG A 188 SHEET 8 AA 8 GLY A 89 TYR A 91 -1 O GLY A 89 N CYS A 104 SHEET 1 AB 5 LYS A 201 THR A 202 0 SHEET 2 AB 5 LYS A 208 HIS A 214 -1 O LEU A 209 N LYS A 201 SHEET 3 AB 5 HIS A 270 LYS A 273 -1 O HIS A 270 N HIS A 214 SHEET 4 AB 5 LEU A 231 THR A 235 -1 O GLN A 232 N ARG A 271 SHEET 5 AB 5 GLY A 238 ASP A 241 -1 O GLY A 238 N THR A 235 LINK NE2 HIS A 214 FE FE A1333 1555 1555 2.21 LINK OD1 ASP A 216 FE FE A1333 1555 1555 2.12 LINK NE2 HIS A 270 FE FE A1333 1555 1555 2.20 LINK S13 M8F A1332 FE FE A1333 1555 1555 2.36 LINK S20 M8F A1332 FE FE A1333 1555 1555 2.57 LINK FE FE A1333 O HOH A2281 1555 1555 2.18 CISPEP 1 ASP A 193 PRO A 194 0 7.91 SITE 1 AC1 22 ARG A 87 TYR A 91 SER A 183 ILE A 187 SITE 2 AC1 22 TYR A 189 PHE A 211 HIS A 214 ASP A 216 SITE 3 AC1 22 LEU A 231 HIS A 270 VAL A 272 SER A 281 SITE 4 AC1 22 PHE A 285 FE A1333 HOH A2281 HOH A2388 SITE 5 AC1 22 HOH A2389 HOH A2390 HOH A2391 HOH A2392 SITE 6 AC1 22 HOH A2393 HOH A2394 SITE 1 AC2 5 HIS A 214 ASP A 216 HIS A 270 M8F A1332 SITE 2 AC2 5 HOH A2281 SITE 1 AC3 4 ALA A 24 ARG A 27 LYS A 80 HOH A2395 SITE 1 AC4 6 ARG A 53 ASP A 140 PHE A 141 HOH A2196 SITE 2 AC4 6 HOH A2396 HOH A2397 SITE 1 AC5 6 ASP A 84 GLN A 85 GLU A 125 VAL A 126 SITE 2 AC5 6 HOH A2398 HOH A2399 CRYST1 46.523 70.882 100.923 90.00 90.00 90.00 P 21 21 21 4 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 0.021495 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014108 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009909 0.00000