HEADER METAL BINDING PROTEIN 18-DEC-01 1KNJ TITLE CO-CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE TITLE 2 SYNTHASE (ISPF) FROM E. COLI INVOLVED IN MEVALONATE-INDEPENDENT TITLE 3 ISOPRENOID BIOSYNTHESIS, COMPLEXED WITH CMP/MECDP/MN2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MECPS; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: ISPF; 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: PHIS8 KEYWDS ISOPRENOIDS, DEOXYXYLULOSE/METHYL-ERYTHRITOL-PHOSPHATE PATHWAY, KEYWDS 2 CYCLODIPHOSPHATE, MEP, YGBB, ISPF, MECDP, 2-C-METHYL-D-ERYTHRITOL-2, KEYWDS 3 4-CYCLODIPHOSPHATE SYNTHASE, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.B.RICHARD,J.L.FERRER,M.E.BOWMAN,A.M.LILLO,C.N.TETZLAFF,D.E.CANE, AUTHOR 2 J.P.NOEL REVDAT 4 06-NOV-24 1KNJ 1 REMARK SEQADV LINK ATOM REVDAT 3 13-JUL-11 1KNJ 1 VERSN REVDAT 2 24-FEB-09 1KNJ 1 VERSN REVDAT 1 18-JUN-02 1KNJ 0 JRNL AUTH S.B.RICHARD,J.L.FERRER,M.E.BOWMAN,A.M.LILLO,C.N.TETZLAFF, JRNL AUTH 2 D.E.CANE,J.P.NOEL JRNL TITL STRUCTURE AND MECHANISM OF 2-C-METHYL-D-ERYTHRITOL JRNL TITL 2 2,4-CYCLODIPHOSPHATE SYNTHASE. AN ENZYME IN THE JRNL TITL 3 MEVALONATE-INDEPENDENT ISOPRENOID BIOSYNTHETIC PATHWAY. JRNL REF J.BIOL.CHEM. V. 277 8667 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 11786530 JRNL DOI 10.1074/JBC.C100739200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.B.RICHARD,M.E.BOWMAN,W.KWIATKOWSKI,I.KANG,C.CHOW, REMARK 1 AUTH 2 A.M.LILLO,D.E.CANE,J.P.NOEL REMARK 1 TITL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL REMARK 1 TITL 2 SYNTHETASE INVOLVED IN MEVALONATE-INDEPENDENT ISOPRENOID REMARK 1 TITL 3 BIOSYNTHESIS REMARK 1 REF NAT.STRUCT.BIOL. V. 8 641 2001 REMARK 1 REFN ISSN 1072-8368 REMARK 1 DOI 10.1038/89691 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1949090.320 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.9 REMARK 3 NUMBER OF REFLECTIONS : 11262 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) : 0.241 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 577 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1495 REMARK 3 BIN R VALUE (WORKING SET) : 0.3340 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 76 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.038 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1166 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 22 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 92.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.46 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.38 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.520 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 41.98 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : LIGAND.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : LIGAND.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KNJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015145. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAR-01; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ESRF; ESRF REMARK 200 BEAMLINE : BM30A; ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795, 0.9800, 0.9724; 0.9340 REMARK 200 MONOCHROMATOR : HORIZONTALLY FOCUSED BY SAGITTAL REMARK 200 CURVED 2ND CRYSTAL; SAGITALLY REMARK 200 FOCUSED GE(220) REMARK 200 OPTICS : MIRRORS; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11923 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.66000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 482.0 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (NH4)2SO4, PEG 400, NAI, PIPES, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y,-Z REMARK 290 16555 X,-Y,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z,-X,-Y+1/2 REMARK 290 19555 -Z,-X+1/2,Y REMARK 290 20555 -Z+1/2,X,-Y REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z,-X REMARK 290 23555 Y,-Z,-X+1/2 REMARK 290 24555 -Y,-Z+1/2,X 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 72.12700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.12700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 72.12700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.12700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 72.12700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 72.12700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 72.12700 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 72.12700 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 72.12700 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 72.12700 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 72.12700 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 72.12700 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 72.12700 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 72.12700 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 72.12700 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 72.12700 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 72.12700 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 72.12700 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 72.12700 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 72.12700 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 72.12700 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 72.12700 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 72.12700 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 72.12700 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 72.12700 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 72.12700 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 72.12700 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 72.12700 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 72.12700 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 72.12700 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 72.12700 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 72.12700 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 72.12700 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 72.12700 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 72.12700 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 72.12700 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A HOMOTRIMER GENERATED FROM THE REMARK 300 MONOMER IN THE ASYMMETRIC UNIT BY THE OPERATIONS: Z,X,Y AND Y,Z,X 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 9660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 403 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 413 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 157 REMARK 465 THR A 158 REMARK 465 LYS A 159 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 PRO A 17 C - N - CA ANGL. DEV. = 11.9 DEGREES REMARK 500 PRO A 62 C - N - CA ANGL. DEV. = 21.0 DEGREES REMARK 500 PRO A 62 C - N - CD ANGL. DEV. = -25.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 8 145.07 -170.55 REMARK 500 GLU A 15 -130.65 -65.48 REMARK 500 PRO A 17 139.88 -20.50 REMARK 500 TYR A 27 140.67 -172.94 REMARK 500 ASP A 56 169.16 33.54 REMARK 500 PHE A 61 158.96 64.00 REMARK 500 PRO A 62 35.26 -142.13 REMARK 500 THR A 64 57.53 38.74 REMARK 500 PRO A 66 86.25 -14.03 REMARK 500 ALA A 67 -61.07 172.42 REMARK 500 LYS A 69 119.68 153.84 REMARK 500 LYS A 87 31.14 -80.53 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 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 8 OD1 REMARK 620 2 ASP A 8 OD2 55.0 REMARK 620 N 1 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C5P A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CDI A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KNK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE REMARK 900 SYNTHASE (ISPF) FROM E. COLI INVOLVED IN MEVALONATE-INDEPENDENT REMARK 900 ISOPRENOID BIOSYNTHESIS DBREF 1KNJ A 1 159 UNP P62617 ISPF_ECOLI 1 159 SEQADV 1KNJ MSE A 1 UNP P62617 MET 1 MODIFIED RESIDUE SEQADV 1KNJ MSE A 105 UNP P62617 MET 105 MODIFIED RESIDUE SEQADV 1KNJ MSE A 112 UNP P62617 MET 112 MODIFIED RESIDUE SEQADV 1KNJ MSE A 124 UNP P62617 MET 124 MODIFIED RESIDUE SEQRES 1 A 159 MSE ARG ILE GLY HIS GLY PHE ASP VAL HIS ALA PHE GLY SEQRES 2 A 159 GLY GLU GLY PRO ILE ILE ILE GLY GLY VAL ARG ILE PRO SEQRES 3 A 159 TYR GLU LYS GLY LEU LEU ALA HIS SER ASP GLY ASP VAL SEQRES 4 A 159 ALA LEU HIS ALA LEU THR ASP ALA LEU LEU GLY ALA ALA SEQRES 5 A 159 ALA LEU GLY ASP ILE GLY LYS LEU PHE PRO ASP THR ASP SEQRES 6 A 159 PRO ALA PHE LYS GLY ALA ASP SER ARG GLU LEU LEU ARG SEQRES 7 A 159 GLU ALA TRP ARG ARG ILE GLN ALA LYS GLY TYR THR LEU SEQRES 8 A 159 GLY ASN VAL ASP VAL THR ILE ILE ALA GLN ALA PRO LYS SEQRES 9 A 159 MSE LEU PRO HIS ILE PRO GLN MSE ARG VAL PHE ILE ALA SEQRES 10 A 159 GLU ASP LEU GLY CYS HIS MSE ASP ASP VAL ASN VAL LYS SEQRES 11 A 159 ALA THR THR THR GLU LYS LEU GLY PHE THR GLY ARG GLY SEQRES 12 A 159 GLU GLY ILE ALA CYS GLU ALA VAL ALA LEU LEU ILE LYS SEQRES 13 A 159 ALA THR LYS MODRES 1KNJ MSE A 1 MET SELENOMETHIONINE MODRES 1KNJ MSE A 105 MET SELENOMETHIONINE MODRES 1KNJ MSE A 112 MET SELENOMETHIONINE MODRES 1KNJ MSE A 124 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 105 8 HET MSE A 112 8 HET MSE A 124 8 HET MN A 401 1 HET C5P A 201 21 HET CDI A 301 16 HETNAM MSE SELENOMETHIONINE HETNAM MN MANGANESE (II) ION HETNAM C5P CYTIDINE-5'-MONOPHOSPHATE HETNAM CDI 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 MN MN 2+ FORMUL 3 C5P C9 H14 N3 O8 P FORMUL 4 CDI C5 H12 O9 P2 FORMUL 5 HOH *22(H2 O) HELIX 1 1 ASP A 38 ALA A 52 1 15 HELIX 2 2 ASP A 56 PHE A 61 5 6 HELIX 3 3 ASP A 72 LYS A 87 1 16 HELIX 4 4 HIS A 108 LEU A 120 1 13 HELIX 5 5 HIS A 123 ASP A 125 5 3 HELIX 6 6 LEU A 137 ARG A 142 1 6 SHEET 1 A 4 ARG A 2 ALA A 11 0 SHEET 2 A 4 GLY A 145 ILE A 155 -1 O ALA A 150 N GLY A 6 SHEET 3 A 4 THR A 90 ILE A 99 -1 N ILE A 99 O ALA A 147 SHEET 4 A 4 VAL A 127 THR A 132 1 O ASN A 128 N VAL A 94 SHEET 1 B 2 ILE A 18 ILE A 20 0 SHEET 2 B 2 VAL A 23 ILE A 25 -1 O ILE A 25 N ILE A 18 LINK C MSE A 1 N ARG A 2 1555 1555 1.33 LINK C LYS A 104 N MSE A 105 1555 1555 1.33 LINK C MSE A 105 N LEU A 106 1555 1555 1.33 LINK C GLN A 111 N MSE A 112 1555 1555 1.34 LINK C MSE A 112 N ARG A 113 1555 1555 1.33 LINK C HIS A 123 N MSE A 124 1555 1555 1.32 LINK C MSE A 124 N ASP A 125 1555 1555 1.33 LINK OD1 ASP A 8 MN MN A 401 1555 1555 2.49 LINK OD2 ASP A 8 MN MN A 401 1555 1555 2.30 CISPEP 1 ALA A 102 PRO A 103 0 -0.66 SITE 1 AC1 4 ASP A 8 HIS A 10 HIS A 42 CDI A 301 SITE 1 AC2 12 ASP A 56 GLY A 58 ALA A 100 PRO A 103 SITE 2 AC2 12 LYS A 104 MSE A 105 LEU A 106 ALA A 131 SITE 3 AC2 12 THR A 132 THR A 133 GLU A 135 CDI A 301 SITE 1 AC3 11 ASP A 8 HIS A 10 ALA A 33 HIS A 34 SITE 2 AC3 11 SER A 35 HIS A 42 ILE A 57 PRO A 62 SITE 3 AC3 11 C5P A 201 MN A 401 HOH A 422 CRYST1 144.254 144.254 144.254 90.00 90.00 90.00 I 21 3 24 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 0.006932 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006932 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006932 0.00000 HETATM 1 N MSE A 1 29.365 29.461 35.766 1.00 78.61 N HETATM 2 CA MSE A 1 30.175 28.377 35.167 1.00 79.59 C HETATM 3 C MSE A 1 29.397 27.064 34.986 1.00 74.41 C HETATM 4 O MSE A 1 29.978 25.975 35.058 1.00 74.59 O HETATM 5 CB MSE A 1 31.438 28.130 36.017 1.00 89.08 C HETATM 6 CG MSE A 1 32.419 29.330 36.117 1.00100.15 C HETATM 7 SE MSE A 1 34.102 29.045 37.157 1.00116.00 SE HETATM 8 CE MSE A 1 35.444 29.207 35.745 1.00110.13 C