HEADER TRANSFERASE 16-MAR-11 2YCM TITLE INHIBITORS OF HERBICIDAL TARGET ISPD COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, COMPND 3 CHLOROPLASTIC; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: CYTIDYLTRANSFERASE DOMAIN, RESIDUES 76-302; COMPND 6 SYNONYM: 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, MEP COMPND 7 CYTIDYLYLTRANSFERASE, ATMECT, ATMEPCT, MCT; COMPND 8 EC: 2.7.7.60; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PREP4; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNCO113 KEYWDS TRANSFERASE, HERBICIDE, ALLOSTERIC BINDING POCKET, NON-MEVALONATE- KEYWDS 2 PATHWAY EXPDTA X-RAY DIFFRACTION AUTHOR H.W.HOEFFKEN REVDAT 2 20-DEC-23 2YCM 1 REMARK REVDAT 1 24-AUG-11 2YCM 0 JRNL AUTH M.C.WITSCHEL,H.W.HOEFFKEN,M.SEET,L.PARRA,T.MIETZNER, JRNL AUTH 2 F.THATER,R.NIGGEWEG,F.ROHL,B.ILLARIONOV,F.ROHDICH,J.KAISER, JRNL AUTH 3 M.FISCHER,A.BACHER,F.DIEDERICH JRNL TITL INHIBITORS OF THE HERBICIDAL TARGET ISPD: ALLOSTERIC SITE JRNL TITL 2 BINDING. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 50 7931 2011 JRNL REFN ISSN 1433-7851 JRNL PMID 21766403 JRNL DOI 10.1002/ANIE.201102281 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.GABRIELSEN,J.KAISER,F.ROHDICH,W.EISENREICH,R.LAUPITZ, REMARK 1 AUTH 2 A.BACHER,C.S.BOND,W.N.HUNTER REMARK 1 TITL THE CRYSTAL STRUCTURE OF A PLANT 2C-METHYL-D- ERYTHRITOL REMARK 1 TITL 2 4-PHOSPHATE CYTIDYLYLTRANSFERASE EXHIBITS A DISTINCT REMARK 1 TITL 3 QUATERNARY STRUCTURE COMPARED TO BACTERIAL HOMOLOGUES AND A REMARK 1 TITL 4 POSSIBLE ROLE IN FEEDBACK REGULATION FOR CYTIDINE REMARK 1 TITL 5 MONOPHOSPHATE. REMARK 1 REF FEBS J. V. 273 1065 2006 REMARK 1 REFN ISSN 1742-464X REMARK 1 PMID 16478479 REMARK 1 DOI 10.1111/J.1742-4658.2006.05133.X REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 73.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 21497 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1132 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1557 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1640 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.49000 REMARK 3 B22 (A**2) : -0.49000 REMARK 3 B33 (A**2) : 0.73000 REMARK 3 B12 (A**2) : -0.24000 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): 0.205 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.095 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.984 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1708 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1114 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2325 ; 1.908 ; 2.003 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2761 ; 1.035 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 214 ; 6.901 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 69 ;38.227 ;26.232 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 295 ;16.425 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;16.879 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 275 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1875 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 302 ; 0.001 ; 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): 1075 ; 1.903 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 428 ; 0.570 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1751 ; 3.124 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 633 ; 4.654 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 574 ; 7.062 ; 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): 2822 ; 2.028 ; 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 : BABINET MODEL WITH 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. THE ELECTRON DENSITY REMARK 3 MAP SUGGESTS THAT IN THE CRYSTAL THE ALLOSTERIC POCKET IS ONLY REMARK 3 PARTIALLY OCCUPIED AND THEREFOR THE ELECTRON DENSITY REFLECTS AN REMARK 3 OVERLAY OF THE UNLIGANDED AND LIGANDED ENZYME. THIS IS IN REMARK 3 ACCORDANCE WITH THE HIGH TEMPERATURE FACTORS OF PART THE LIGAND REMARK 3 AND OF THE AMINO ACIDS 264 TO 268 WHICH HAVE TO MOVE TO OPEN THE REMARK 3 ALLOSTERIC BINDING POCKET. REMARK 4 REMARK 4 2YCM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1290047714. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.939272 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 : 22629 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 36.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 1.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.430 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 2YC3 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NATIVE CRYSTALS (SEE REMARK 1, PDB REMARK 280 1W77) WERE SOAKED WITH A SATURATED SOLUTION OF LIGAND REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 37.53000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 21.66796 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 73.60667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 37.53000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 21.66796 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 73.60667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 37.53000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 21.66796 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 73.60667 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 37.53000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 21.66796 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 73.60667 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 37.53000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 21.66796 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 73.60667 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 37.53000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 21.66796 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 73.60667 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 43.33591 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 147.21333 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 43.33591 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 147.21333 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 43.33591 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 147.21333 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 43.33591 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 147.21333 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 43.33591 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 147.21333 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 43.33591 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 147.21333 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 130.00773 REMARK 350 BIOMT3 2 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 GLY A 87 REMARK 465 GLN A 88 REMARK 465 GLY A 89 REMARK 465 LYS A 90 REMARK 465 ARG A 91 REMARK 465 MET A 92 REMARK 465 LYS A 93 REMARK 465 MET A 94 REMARK 465 SER A 95 REMARK 465 ASP A 227 REMARK 465 ARG A 228 REMARK 465 LYS A 229 REMARK 465 ASP A 301 REMARK 465 SER A 302 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 LYS A 98 CG CD CE NZ REMARK 470 LEU A 226 CG CD1 CD2 REMARK 470 THR A 286 OG1 CG2 REMARK 470 THR A 287 OG1 CG2 REMARK 470 PRO A 288 CG CD REMARK 470 ASP A 289 CG OD1 OD2 REMARK 470 LEU A 292 CG CD1 CD2 REMARK 470 ARG A 296 CG CD NE CZ NH1 NH2 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 OD2 ASP A 179 O HOH A 2042 1.87 REMARK 500 O HOH A 2033 O HOH A 2034 1.88 REMARK 500 OE2 GLU A 267 O HOH A 2080 1.92 REMARK 500 O3 30A A 1306 O HOH A 2093 1.94 REMARK 500 OD2 ASP A 261 O HOH A 2080 2.06 REMARK 500 OD1 ASP A 135 O HOH A 2012 2.11 REMARK 500 OE2 GLU A 167 CD CD A 1303 2.12 REMARK 500 OD1 ASP A 159 O HOH A 2033 2.17 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 2018 O HOH A 2024 5675 1.94 REMARK 500 OE2 GLU A 121 CD CD A 1302 2665 2.07 REMARK 500 O HOH A 2028 O HOH A 2039 5675 2.08 REMARK 500 OE2 GLU A 191 CD CD A 1302 2665 2.18 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 173 CB GLU A 173 CG 0.153 REMARK 500 GLU A 173 CG GLU A 173 CD 0.092 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 LYS A 77 52.10 34.46 REMARK 500 LEU A 104 53.99 35.51 REMARK 500 ASP A 145 46.25 -91.84 REMARK 500 GLN A 235 -163.57 -121.49 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 CD A1301 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 138 OE2 REMARK 620 2 GLU A 138 OE2 162.0 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 CD A 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 1302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 1303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 1305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 30A A 1306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1W77 RELATED DB: PDB REMARK 900 2C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE ( ISPD) REMARK 900 FROM ARABIDOPSIS THALIANA REMARK 900 RELATED ID: 2YC3 RELATED DB: PDB REMARK 900 INHIBITORS OF THE HERBICIDAL TARGET ISPD REMARK 900 RELATED ID: 2YC5 RELATED DB: PDB REMARK 900 INHIBITORS OF THE HERBICIDAL TARGET ISPD DBREF 2YCM A 76 302 UNP P69834 ISPD_ARATH 76 302 SEQADV 2YCM SER A 149 UNP P69834 ARG 149 CONFLICT SEQRES 1 A 227 GLU LYS SER VAL SER VAL ILE LEU LEU ALA GLY GLY GLN SEQRES 2 A 227 GLY LYS ARG MET LYS MET SER MET PRO LYS GLN TYR ILE SEQRES 3 A 227 PRO LEU LEU GLY GLN PRO ILE ALA LEU TYR SER PHE PHE SEQRES 4 A 227 THR PHE SER ARG MET PRO GLU VAL LYS GLU ILE VAL VAL SEQRES 5 A 227 VAL CYS ASP PRO PHE PHE ARG ASP ILE PHE GLU GLU TYR SEQRES 6 A 227 GLU GLU SER ILE ASP VAL ASP LEU SER PHE ALA ILE PRO SEQRES 7 A 227 GLY LYS GLU ARG GLN ASP SER VAL TYR SER GLY LEU GLN SEQRES 8 A 227 GLU ILE ASP VAL ASN SER GLU LEU VAL CYS ILE HIS ASP SEQRES 9 A 227 SER ALA ARG PRO LEU VAL ASN THR GLU ASP VAL GLU LYS SEQRES 10 A 227 VAL LEU LYS ASP GLY SER ALA VAL GLY ALA ALA VAL LEU SEQRES 11 A 227 GLY VAL PRO ALA LYS ALA THR ILE LYS GLU VAL ASN SER SEQRES 12 A 227 ASP SER LEU VAL VAL LYS THR LEU ASP ARG LYS THR LEU SEQRES 13 A 227 TRP GLU MET GLN THR PRO GLN VAL ILE LYS PRO GLU LEU SEQRES 14 A 227 LEU LYS LYS GLY PHE GLU LEU VAL LYS SER GLU GLY LEU SEQRES 15 A 227 GLU VAL THR ASP ASP VAL SER ILE VAL GLU TYR LEU LYS SEQRES 16 A 227 HIS PRO VAL TYR VAL SER GLN GLY SER TYR THR ASN ILE SEQRES 17 A 227 LYS VAL THR THR PRO ASP ASP LEU LEU LEU ALA GLU ARG SEQRES 18 A 227 ILE LEU SER GLU ASP SER HET CD A1301 1 HET CD A1302 1 HET CD A1303 1 HET NA A1304 1 HET CU A1305 1 HET 30A A1306 21 HETNAM CD CADMIUM ION HETNAM NA SODIUM ION HETNAM CU COPPER (II) ION HETNAM 30A 6-BENZYL-5-CHLORO-7-HYDROXYPYRAZOLO[1,5-A]PYRIMIDINE-3- HETNAM 2 30A CARBOXYLIC ACID FORMUL 2 CD 3(CD 2+) FORMUL 5 NA NA 1+ FORMUL 6 CU CU 2+ FORMUL 7 30A C14 H10 CL N3 O3 FORMUL 8 HOH *93(H2 O) HELIX 1 1 PRO A 97 TYR A 100 5 4 HELIX 2 2 ILE A 108 ARG A 118 1 11 HELIX 3 3 ASP A 130 PHE A 132 5 3 HELIX 4 4 PHE A 133 GLU A 139 1 7 HELIX 5 5 TYR A 140 ILE A 144 5 5 HELIX 6 6 GLU A 156 GLN A 166 1 11 HELIX 7 7 ASN A 186 GLY A 201 1 16 HELIX 8 8 LYS A 241 GLY A 256 1 16 HELIX 9 9 VAL A 263 LEU A 269 1 7 HELIX 10 10 THR A 287 GLU A 300 1 14 SHEET 1 AA 7 ASP A 147 ALA A 151 0 SHEET 2 AA 7 VAL A 122 VAL A 128 1 O LYS A 123 N ASP A 147 SHEET 3 AA 7 VAL A 79 LEU A 84 1 O VAL A 79 N LYS A 123 SHEET 4 AA 7 LEU A 174 ASP A 179 1 O LEU A 174 N SER A 80 SHEET 5 AA 7 TRP A 232 ILE A 240 -1 O GLN A 238 N ILE A 177 SHEET 6 AA 7 ALA A 202 PRO A 208 -1 O ALA A 203 N VAL A 239 SHEET 7 AA 7 TYR A 274 GLN A 277 1 O TYR A 274 N VAL A 204 SHEET 1 AB 2 PRO A 102 LEU A 103 0 SHEET 2 AB 2 GLN A 106 PRO A 107 -1 O GLN A 106 N LEU A 103 SHEET 1 AC 2 GLU A 215 VAL A 216 0 SHEET 2 AC 2 VAL A 222 VAL A 223 -1 O VAL A 223 N GLU A 215 LINK OE2 GLU A 138 CD CD A1301 1555 5675 1.82 LINK OE2 GLU A 138 CD CD A1301 5675 1555 1.82 CISPEP 1 THR A 236 PRO A 237 0 9.51 SITE 1 AC1 5 LYS A 123 GLU A 138 GLU A 141 ASP A 169 SITE 2 AC1 5 HOH A2017 SITE 1 AC2 4 GLU A 121 GLU A 191 HIS A 271 HOH A2081 SITE 1 AC3 1 GLU A 167 SITE 1 AC4 2 GLU A 139 HOH A2015 SITE 1 AC5 1 ASP A 290 SITE 1 AC6 14 ARG A 157 GLN A 158 ILE A 177 ALA A 203 SITE 2 AC6 14 GLN A 238 VAL A 259 ASP A 261 ASP A 262 SITE 3 AC6 14 VAL A 263 SER A 264 ILE A 265 VAL A 266 SITE 4 AC6 14 VAL A 273 HOH A2093 CRYST1 75.060 75.060 220.820 90.00 90.00 120.00 H 3 2 18 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 0.013323 0.007692 0.000000 0.00000 SCALE2 0.000000 0.015384 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004529 0.00000