HEADER ISOMERASE 06-FEB-08 2VNP TITLE MONOCLINIC FORM OF IDI-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ISOPENTENYL DIPHOSPHATE ISOMERASE, IPP ISOMERASE,; COMPND 5 EC: 5.3.3.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 511693; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS ISOPRENE BIOSYNTHESIS, POLYMORPHISM, METAL-BINDING, IPP ISOMERASE, KEYWDS 2 MANGANESE, CYTOPLASM, ISOMERASE, MAGNESIUM EXPDTA X-RAY DIFFRACTION AUTHOR J.DE RUYCK,Y.OUDJAMA,J.WOUTERS REVDAT 4 13-DEC-23 2VNP 1 LINK REVDAT 3 24-FEB-09 2VNP 1 VERSN REVDAT 2 06-MAY-08 2VNP 1 JRNL REMARK REVDAT 1 18-MAR-08 2VNP 0 SPRSDE 18-MAR-08 2VNP 2VEH JRNL AUTH J.DE RUYCK,Y.OUDJAMA,J.WOUTERS JRNL TITL MONOCLINIC FORM OF ISOPENTENYL DIPHOSPHATE ISOMERASE: A CASE JRNL TITL 2 OF POLYMORPHISM IN BIOMOLECULAR CRYSTALS. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 64 239 2008 JRNL REFN ESSN 1744-3091 JRNL PMID 18391416 JRNL DOI 10.1107/S174430910800568X REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 17426 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 941 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) : 2.19 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.24 REMARK 3 REFLECTION IN BIN (WORKING SET) : 967 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2821 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.310 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.234 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.159 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.111 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.898 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2921 ; 0.026 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3989 ; 2.092 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 354 ; 7.472 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;33.794 ;23.285 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 454 ;16.114 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;19.483 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 436 ; 0.146 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2240 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1404 ; 0.229 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1941 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 133 ; 0.157 ; 0.200 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): 38 ; 0.229 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.226 ; 0.200 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): 1843 ; 1.175 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2878 ; 1.775 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1277 ; 2.910 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1111 ; 4.026 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 4 A 179 4 REMARK 3 1 B 4 B 179 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1393 ; 0.52 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1393 ; 1.55 ; 2.00 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 2VNP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1290035262. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9797 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18119 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.16000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1HX3 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.5 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 34.55000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: PQS 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: PQS 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 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 GLN A 2 REMARK 465 THR A 3 REMARK 465 GLN A 180 REMARK 465 LEU A 181 REMARK 465 LYS A 182 REMARK 465 LEU A 183 REMARK 465 MET B 1 REMARK 465 GLN B 2 REMARK 465 THR B 3 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 CYS A 142 CB CYS A 142 SG -0.106 REMARK 500 GLU B 4 CG GLU B 4 CD 0.119 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 169 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 172 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 172 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 LEU B 19 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 ARG B 85 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 105 NE - CZ - NH1 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 ASP A 28 35.92 -150.59 REMARK 500 THR A 29 123.66 -33.70 REMARK 500 TYR A 99 84.47 -158.04 REMARK 500 ASN B 64 -173.10 -64.09 REMARK 500 TYR B 99 67.79 -162.50 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 A1180 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 25 NE2 REMARK 620 2 HIS A 32 NE2 90.7 REMARK 620 3 HIS A 69 NE2 94.1 95.4 REMARK 620 4 GLU A 114 OE1 90.1 160.0 104.5 REMARK 620 5 GLU A 114 OE2 92.6 101.1 162.1 58.9 REMARK 620 6 GLU A 116 OE2 170.9 97.4 89.2 80.9 81.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1181 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 67 O REMARK 620 2 GLU A 87 OE2 94.3 REMARK 620 3 DED A1182 O6 91.7 172.2 REMARK 620 4 DED A1182 O2 102.7 92.2 81.6 REMARK 620 5 HOH A2008 O 82.4 93.4 92.3 172.1 REMARK 620 6 HOH A2017 O 162.0 83.4 92.3 95.1 80.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B1184 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 25 NE2 REMARK 620 2 HIS B 32 NE2 91.2 REMARK 620 3 HIS B 69 NE2 86.1 106.3 REMARK 620 4 GLU B 114 OE1 83.9 145.7 107.1 REMARK 620 5 GLU B 114 OE2 97.2 89.0 164.3 58.3 REMARK 620 6 GLU B 116 OE2 167.6 100.0 85.5 89.8 88.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1185 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 67 O REMARK 620 2 GLU B 87 OE2 100.7 REMARK 620 3 DED B1186 O1 101.0 81.4 REMARK 620 4 DED B1186 O6 83.7 167.1 85.8 REMARK 620 5 HOH B2015 O 75.9 102.6 175.2 90.2 REMARK 620 6 HOH B2025 O 168.1 85.5 89.9 92.4 92.9 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 A1180 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1181 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DED A1182 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B1184 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1185 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DED B1186 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NFS RELATED DB: PDB REMARK 900 STRUCTURE AND MECHANISM OF ACTION OFISOPENTENYLPYROPHOSPHATE- REMARK 900 DIMETHYLALLYLPYROPHOSPHATEISOMERASE: COMPLEX WITH NIPP REMARK 900 RELATED ID: 1Q54 RELATED DB: PDB REMARK 900 STRUCTURE AND MECHANISM OF ACTION OFISOPENTENYLPYROPHOSPHATE- REMARK 900 DIMETHYLALLYLPYROPHOSPHATEISOMERASE: COMPLEX WITH THE BROMOHYDRINE REMARK 900 OF IPP REMARK 900 RELATED ID: 1PPV RELATED DB: PDB REMARK 900 ISOPENTENYLPYROPHOSPHATE- DIMETHYLALLYLPYROPHOSPHATEISOMERASE IN REMARK 900 COMPLEX WITH THE BROMOHYDRINE OF IPP REMARK 900 RELATED ID: 1OW2 RELATED DB: PDB REMARK 900 STRUCTURE AND MECHANISM OF ACTION OFISOPENTENYLPYROPHOSPHATE- REMARK 900 DIMETHYLALLYLPYROPHOSPHATEISOMERASE: COMPLEX OF C67A MUTANT WITH REMARK 900 EIPP REMARK 900 RELATED ID: 1PPW RELATED DB: PDB REMARK 900 ISOPENTENYLPYROPHOSPHATE- DIMETHYLALLYLPYROPHOSPHATEISOMERASE IN REMARK 900 COMPLEX WITH THE BROMOHYDRINE OF IPP REMARK 900 RELATED ID: 1X84 RELATED DB: PDB REMARK 900 IPP ISOMERASE (WT) REACTED WITH (S)- BROMOHYDRINE OF IPP REMARK 900 RELATED ID: 1I9A RELATED DB: PDB REMARK 900 STRUCTURAL STUDIES OF CHOLESTEROL BIOSYNTHESIS : MEVALONATE5- REMARK 900 DIPHOSPHATE DECARBOXYLASE AND ISOPENTENYL DIPHOSPHATEISOMERASE REMARK 900 RELATED ID: 1NFZ RELATED DB: PDB REMARK 900 STRUCTURE AND MECHANISM OF ACTION OFISOPENTENYLPYROPHOSPHATE- REMARK 900 DIMETHYLALLYLPYROPHOSPHATEISOMERASE: COMPLEX WITH EIPP REMARK 900 RELATED ID: 1R67 RELATED DB: PDB REMARK 900 Y104A MUTANT OF E.COLI IPP ISOMERASE REMARK 900 RELATED ID: 1X83 RELATED DB: PDB REMARK 900 Y104F IPP ISOMERASE REACTED WITH (S)- BROMOHYDRINE OF IPP REMARK 900 RELATED ID: 1HX3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E.COLI ISOPENTENYLDIPHOSPHATE:DIMETHYLALLYL REMARK 900 DIPHOSPHATE ISOMERASE REMARK 900 RELATED ID: 1HZT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF METAL-FREE ISOPENTENYLDIPHOSPHATE: REMARK 900 DIMETHYLALLYL DIPHOSPHATE ISOMERASE REMARK 900 RELATED ID: 1PVF RELATED DB: PDB REMARK 900 E.COLI IPP ISOMERASE IN COMPLEX WITH DIPHOSPHATE REMARK 900 RELATED ID: 2VNQ RELATED DB: PDB REMARK 900 MONOCLINIC FORM OF IDI-1 DBREF 2VNP A 1 182 UNP Q46822 IDI_ECOLI 1 182 DBREF 2VNP A 183 183 PDB 2VNP 2VNP 183 183 DBREF 2VNP B 1 182 UNP Q46822 IDI_ECOLI 1 182 DBREF 2VNP B 183 183 PDB 2VNP 2VNP 183 183 SEQRES 1 A 183 MET GLN THR GLU HIS VAL ILE LEU LEU ASN ALA GLN GLY SEQRES 2 A 183 VAL PRO THR GLY THR LEU GLU LYS TYR ALA ALA HIS THR SEQRES 3 A 183 ALA ASP THR ARG LEU HIS LEU ALA PHE SER SER TRP LEU SEQRES 4 A 183 PHE ASN ALA LYS GLY GLN LEU LEU VAL THR ARG ARG ALA SEQRES 5 A 183 LEU SER LYS LYS ALA TRP PRO GLY VAL TRP THR ASN SER SEQRES 6 A 183 VAL CYS GLY HIS PRO GLN LEU GLY GLU SER ASN GLU ASP SEQRES 7 A 183 ALA VAL ILE ARG ARG CYS ARG TYR GLU LEU GLY VAL GLU SEQRES 8 A 183 ILE THR PRO PRO GLU SER ILE TYR PRO ASP PHE ARG TYR SEQRES 9 A 183 ARG ALA THR ASP PRO SER GLY ILE VAL GLU ASN GLU VAL SEQRES 10 A 183 CYS PRO VAL PHE ALA ALA ARG THR THR SER ALA LEU GLN SEQRES 11 A 183 ILE ASN ASP ASP GLU VAL MET ASP TYR GLN TRP CYS ASP SEQRES 12 A 183 LEU ALA ASP VAL LEU HIS GLY ILE ASP ALA THR PRO TRP SEQRES 13 A 183 ALA PHE SER PRO TRP MET VAL MET GLN ALA THR ASN ARG SEQRES 14 A 183 GLU ALA ARG LYS ARG LEU SER ALA PHE THR GLN LEU LYS SEQRES 15 A 183 LEU SEQRES 1 B 183 MET GLN THR GLU HIS VAL ILE LEU LEU ASN ALA GLN GLY SEQRES 2 B 183 VAL PRO THR GLY THR LEU GLU LYS TYR ALA ALA HIS THR SEQRES 3 B 183 ALA ASP THR ARG LEU HIS LEU ALA PHE SER SER TRP LEU SEQRES 4 B 183 PHE ASN ALA LYS GLY GLN LEU LEU VAL THR ARG ARG ALA SEQRES 5 B 183 LEU SER LYS LYS ALA TRP PRO GLY VAL TRP THR ASN SER SEQRES 6 B 183 VAL CYS GLY HIS PRO GLN LEU GLY GLU SER ASN GLU ASP SEQRES 7 B 183 ALA VAL ILE ARG ARG CYS ARG TYR GLU LEU GLY VAL GLU SEQRES 8 B 183 ILE THR PRO PRO GLU SER ILE TYR PRO ASP PHE ARG TYR SEQRES 9 B 183 ARG ALA THR ASP PRO SER GLY ILE VAL GLU ASN GLU VAL SEQRES 10 B 183 CYS PRO VAL PHE ALA ALA ARG THR THR SER ALA LEU GLN SEQRES 11 B 183 ILE ASN ASP ASP GLU VAL MET ASP TYR GLN TRP CYS ASP SEQRES 12 B 183 LEU ALA ASP VAL LEU HIS GLY ILE ASP ALA THR PRO TRP SEQRES 13 B 183 ALA PHE SER PRO TRP MET VAL MET GLN ALA THR ASN ARG SEQRES 14 B 183 GLU ALA ARG LYS ARG LEU SER ALA PHE THR GLN LEU LYS SEQRES 15 B 183 LEU HET MN A1180 1 HET MG A1181 1 HET DED A1182 14 HET MN B1184 1 HET MG B1185 1 HET DED B1186 14 HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM DED 2-DIMETHYLAMINO-ETHYL-DIPHOSPHATE FORMUL 3 MN 2(MN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 DED 2(C4 H13 N O7 P2) FORMUL 9 HOH *61(H2 O) HELIX 1 1 LYS A 21 HIS A 25 1 5 HELIX 2 2 SER A 75 GLY A 89 1 15 HELIX 3 3 ASP A 143 THR A 154 1 12 HELIX 4 4 PRO A 155 ALA A 157 5 3 HELIX 5 5 SER A 159 ASN A 168 1 10 HELIX 6 6 ASN A 168 THR A 179 1 12 HELIX 7 7 LYS B 21 HIS B 25 1 5 HELIX 8 8 SER B 75 GLY B 89 1 15 HELIX 9 9 ASP B 143 THR B 154 1 12 HELIX 10 10 PRO B 155 ALA B 157 5 3 HELIX 11 11 SER B 159 ASN B 168 1 10 HELIX 12 12 ASN B 168 PHE B 178 1 11 SHEET 1 AA 2 HIS A 5 LEU A 9 0 SHEET 2 AA 2 PRO A 15 GLU A 20 -1 N THR A 16 O LEU A 8 SHEET 1 AB 3 HIS A 32 LEU A 33 0 SHEET 2 AB 3 VAL A 113 VAL A 117 1 O ASN A 115 N HIS A 32 SHEET 3 AB 3 ARG A 103 THR A 107 -1 O TYR A 104 N GLU A 116 SHEET 1 AC 4 VAL A 66 GLY A 68 0 SHEET 2 AC 4 PHE A 35 PHE A 40 -1 O PHE A 35 N GLY A 68 SHEET 3 AC 4 VAL A 120 ARG A 124 1 O PHE A 121 N TRP A 38 SHEET 4 AC 4 GLU A 96 TYR A 99 -1 O GLU A 96 N ALA A 122 SHEET 1 AD 3 TRP A 62 THR A 63 0 SHEET 2 AD 3 LEU A 46 ARG A 51 -1 O THR A 49 N THR A 63 SHEET 3 AD 3 VAL A 136 CYS A 142 -1 N MET A 137 O ARG A 50 SHEET 1 BA 2 HIS B 5 LEU B 9 0 SHEET 2 BA 2 PRO B 15 GLU B 20 -1 N THR B 16 O LEU B 8 SHEET 1 BB 3 HIS B 32 LEU B 33 0 SHEET 2 BB 3 VAL B 113 VAL B 117 1 O ASN B 115 N HIS B 32 SHEET 3 BB 3 ARG B 103 THR B 107 -1 O TYR B 104 N GLU B 116 SHEET 1 BC 4 VAL B 66 GLY B 68 0 SHEET 2 BC 4 PHE B 35 PHE B 40 -1 O PHE B 35 N GLY B 68 SHEET 3 BC 4 VAL B 120 ARG B 124 1 O PHE B 121 N TRP B 38 SHEET 4 BC 4 GLU B 96 TYR B 99 -1 O GLU B 96 N ALA B 122 SHEET 1 BD 3 TRP B 62 THR B 63 0 SHEET 2 BD 3 LEU B 46 ARG B 51 -1 O THR B 49 N THR B 63 SHEET 3 BD 3 VAL B 136 CYS B 142 -1 N MET B 137 O ARG B 50 LINK NE2 HIS A 25 MN MN A1180 1555 1555 2.18 LINK NE2 HIS A 32 MN MN A1180 1555 1555 2.17 LINK O CYS A 67 MG MG A1181 1555 1555 2.13 LINK NE2 HIS A 69 MN MN A1180 1555 1555 2.04 LINK OE2 GLU A 87 MG MG A1181 1555 1555 2.10 LINK OE1 GLU A 114 MN MN A1180 1555 1555 2.29 LINK OE2 GLU A 114 MN MN A1180 1555 1555 2.02 LINK OE2 GLU A 116 MN MN A1180 1555 1555 1.95 LINK MG MG A1181 O6 DED A1182 1555 1555 2.25 LINK MG MG A1181 O2 DED A1182 1555 1555 2.33 LINK MG MG A1181 O HOH A2008 1555 1555 2.27 LINK MG MG A1181 O HOH A2017 1555 1555 2.44 LINK NE2 HIS B 25 MN MN B1184 1555 1555 2.35 LINK NE2 HIS B 32 MN MN B1184 1555 1555 2.14 LINK O CYS B 67 MG MG B1185 1555 1555 2.14 LINK NE2 HIS B 69 MN MN B1184 1555 1555 2.01 LINK OE2 GLU B 87 MG MG B1185 1555 1555 2.00 LINK OE1 GLU B 114 MN MN B1184 1555 1555 2.36 LINK OE2 GLU B 114 MN MN B1184 1555 1555 2.06 LINK OE2 GLU B 116 MN MN B1184 1555 1555 1.87 LINK MG MG B1185 O1 DED B1186 1555 1555 2.22 LINK MG MG B1185 O6 DED B1186 1555 1555 2.25 LINK MG MG B1185 O HOH B2015 1555 1555 2.48 LINK MG MG B1185 O HOH B2025 1555 1555 2.23 SITE 1 AC1 5 HIS A 25 HIS A 32 HIS A 69 GLU A 114 SITE 2 AC1 5 GLU A 116 SITE 1 AC2 5 CYS A 67 GLU A 87 DED A1182 HOH A2008 SITE 2 AC2 5 HOH A2017 SITE 1 AC3 15 LYS A 21 ALA A 34 ARG A 51 LYS A 55 SITE 2 AC3 15 CYS A 67 GLY A 68 HIS A 69 ARG A 83 SITE 3 AC3 15 GLU A 87 TYR A 104 GLU A 114 GLU A 116 SITE 4 AC3 15 MG A1181 HOH A2028 HOH A2029 SITE 1 AC4 5 HIS B 25 HIS B 32 HIS B 69 GLU B 114 SITE 2 AC4 5 GLU B 116 SITE 1 AC5 5 CYS B 67 GLU B 87 DED B1186 HOH B2015 SITE 2 AC5 5 HOH B2025 SITE 1 AC6 16 LYS B 21 ALA B 34 SER B 36 ARG B 51 SITE 2 AC6 16 LYS B 55 CYS B 67 GLY B 68 HIS B 69 SITE 3 AC6 16 ARG B 83 GLU B 87 TYR B 104 GLU B 114 SITE 4 AC6 16 GLU B 116 MG B1185 HOH B2031 HOH B2032 CRYST1 43.200 69.100 62.400 90.00 100.30 90.00 P 1 21 1 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 0.023148 0.000000 0.004207 0.00000 SCALE2 0.000000 0.014472 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016288 0.00000