HEADER TRANSFERASE 23-DEC-16 5MRO TITLE ARABIDOPSIS THALIANA ISPD GLU258ALA MUTANT IN COMPLEX WITH TITLE 2 AZOLOPYRIMIDINE (1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, COMPND 3 CHLOROPLASTIC; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE,MEP COMPND 6 CYTIDYLYLTRANSFERASE,ATMEPCT; COMPND 7 EC: 2.7.7.60; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: TRUNCATED MUTANT (DELTA 1-74 / R149S) GLU258ALA-MUTANT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: ISPD, MCT, MECT, MEPCT, AT2G02500, T8K22.20; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HERBICIDE, ANTI-INFECTIVES, DRUG DISCOVERY, ALLOSTERIC INHIBITION, KEYWDS 2 MUTANT, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.SCHWAB,B.ILLARIONOV,A.FRANK,A.KUNFERMANN,M.SEET,A.BACHER, AUTHOR 2 M.WITSCHEL,M.FISCHER,M.GROLL,F.DIEDERICH REVDAT 3 17-JAN-24 5MRO 1 LINK REVDAT 2 30-AUG-17 5MRO 1 JRNL REVDAT 1 19-JUL-17 5MRO 0 JRNL AUTH A.SCHWAB,B.ILLARIONOV,A.FRANK,A.KUNFERMANN,M.SEET,A.BACHER, JRNL AUTH 2 M.C.WITSCHEL,M.FISCHER,M.GROLL,F.DIEDERICH JRNL TITL MECHANISM OF ALLOSTERIC INHIBITION OF THE ENZYME ISPD BY JRNL TITL 2 THREE DIFFERENT CLASSES OF LIGANDS. JRNL REF ACS CHEM. BIOL. V. 12 2132 2017 JRNL REFN ESSN 1554-8937 JRNL PMID 28686408 JRNL DOI 10.1021/ACSCHEMBIO.7B00004 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 21461 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1130 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) : 1529 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.2520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1680 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 134 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.31000 REMARK 3 B22 (A**2) : -0.31000 REMARK 3 B33 (A**2) : 1.00000 REMARK 3 B12 (A**2) : -0.15000 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): 0.226 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.121 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.445 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1739 ; 0.007 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1704 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2360 ; 1.296 ; 2.014 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3946 ; 0.898 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 213 ; 5.832 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 69 ;34.052 ;25.652 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 311 ;14.156 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;10.733 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 280 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1892 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 336 ; 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): 859 ; 1.605 ; 3.030 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 857 ; 1.575 ; 3.029 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1069 ; 1.835 ; 4.528 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1070 ; 1.856 ; 4.532 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 879 ; 1.776 ; 3.495 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 880 ; 1.775 ; 3.493 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1291 ; 1.666 ; 5.063 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1919 ; 2.732 ;37.267 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1900 ; 2.589 ;37.011 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3437 ; 0.678 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 74 ;22.223 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3478 ; 5.424 ; 5.000 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 76 A 299 REMARK 3 ORIGIN FOR THE GROUP (A): 12.1034 25.2356 -20.2456 REMARK 3 T TENSOR REMARK 3 T11: 0.0630 T22: 0.0563 REMARK 3 T33: 0.1027 T12: 0.0480 REMARK 3 T13: -0.0064 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 0.3103 L22: 0.4212 REMARK 3 L33: 0.2026 L12: 0.3482 REMARK 3 L13: 0.0692 L23: 0.0040 REMARK 3 S TENSOR REMARK 3 S11: -0.0022 S12: 0.0001 S13: -0.1773 REMARK 3 S21: 0.0427 S22: 0.0301 S23: -0.2034 REMARK 3 S31: -0.1078 S32: -0.0901 S33: -0.0278 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5MRO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1200002899. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22644 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.2000 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 : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.51800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.200 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: 2YC5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM HEPES, 50 MM CDSO4, 800 MM KAC, REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 37.40000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 21.59290 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 73.99667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 37.40000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 21.59290 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 73.99667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 37.40000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 21.59290 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 73.99667 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 37.40000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 21.59290 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 73.99667 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 37.40000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 21.59290 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 73.99667 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 37.40000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 21.59290 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 73.99667 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 43.18580 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 147.99333 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 43.18580 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 147.99333 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 43.18580 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 147.99333 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 43.18580 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 147.99333 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 43.18580 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 147.99333 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 43.18580 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 147.99333 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: 4770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 43.18580 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -73.99667 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 521 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 633 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 MET A 75 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 GLU A 300 REMARK 465 ASP A 301 REMARK 465 SER A 302 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 588 O HOH A 588 4555 1.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 85 43.19 -140.61 REMARK 500 ASP A 145 50.89 -99.77 REMARK 500 GLN A 235 -162.79 -123.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 633 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A 634 DISTANCE = 7.97 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 CD A 407 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 121 OE1 REMARK 620 2 GLU A 121 OE2 52.9 REMARK 620 3 GLU A 191 OE2 95.9 122.7 REMARK 620 4 HIS A 271 ND1 66.0 37.4 88.8 REMARK 620 5 ACT A 403 O 108.7 143.0 87.9 173.4 REMARK 620 6 ACT A 403 OXT 90.5 94.8 136.9 131.9 50.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 406 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 138 OE2 REMARK 620 2 GLU A 141 OE1 82.1 REMARK 620 3 GLU A 141 OE2 87.4 52.5 REMARK 620 4 ASP A 169 OD1 102.6 89.0 37.6 REMARK 620 5 HOH A 578 O 104.2 79.4 29.5 10.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 405 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 167 OE1 REMARK 620 2 GLU A 167 OE2 58.6 REMARK 620 3 HOH A 588 O 142.7 84.2 REMARK 620 4 HOH A 588 O 149.0 102.2 29.6 REMARK 620 5 HOH A 612 O 103.7 109.1 90.1 105.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 404 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 290 OD1 REMARK 620 2 ASP A 290 OD2 39.4 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 Q9P A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 407 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1W77 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF A PLANT 2C-METHYL-D-ERYTHRITOL 4-PHOSPHATE REMARK 900 CYTIDYLYLTRANSFERASE EXHIBITS A DISTINCT QUATERNARY STRUCTURE REMARK 900 COMPARED TO BACTERIAL HOMOLOGUES AND A POSSIBLE ROLE IN FEEDBACK REMARK 900 REGULATION FOR CYTIDINE MONOPHOSPHATE. REMARK 900 RELATED ID: 2YC5 RELATED DB: PDB REMARK 900 INHIBITORS OF THE HERBICIDAL TARGET ISPD: ALLOSTERIC SITE BINDING. REMARK 900 RELATED ID: 4NAK RELATED DB: PDB REMARK 900 ARABIDOPSIS THALIANA ISPD IN COMPLEX WITH PENTABROMO-PSEUDILIN DBREF 5MRO A 76 302 UNP P69834 ISPD_ARATH 76 302 SEQADV 5MRO MET A 75 UNP P69834 INITIATING METHIONINE SEQADV 5MRO SER A 149 UNP P69834 ARG 149 CONFLICT SEQADV 5MRO ALA A 258 UNP P69834 GLU 258 ENGINEERED MUTATION SEQRES 1 A 228 MET GLU LYS SER VAL SER VAL ILE LEU LEU ALA GLY GLY SEQRES 2 A 228 GLN GLY LYS ARG MET LYS MET SER MET PRO LYS GLN TYR SEQRES 3 A 228 ILE PRO LEU LEU GLY GLN PRO ILE ALA LEU TYR SER PHE SEQRES 4 A 228 PHE THR PHE SER ARG MET PRO GLU VAL LYS GLU ILE VAL SEQRES 5 A 228 VAL VAL CYS ASP PRO PHE PHE ARG ASP ILE PHE GLU GLU SEQRES 6 A 228 TYR GLU GLU SER ILE ASP VAL ASP LEU SER PHE ALA ILE SEQRES 7 A 228 PRO GLY LYS GLU ARG GLN ASP SER VAL TYR SER GLY LEU SEQRES 8 A 228 GLN GLU ILE ASP VAL ASN SER GLU LEU VAL CYS ILE HIS SEQRES 9 A 228 ASP SER ALA ARG PRO LEU VAL ASN THR GLU ASP VAL GLU SEQRES 10 A 228 LYS VAL LEU LYS ASP GLY SER ALA VAL GLY ALA ALA VAL SEQRES 11 A 228 LEU GLY VAL PRO ALA LYS ALA THR ILE LYS GLU VAL ASN SEQRES 12 A 228 SER ASP SER LEU VAL VAL LYS THR LEU ASP ARG LYS THR SEQRES 13 A 228 LEU TRP GLU MET GLN THR PRO GLN VAL ILE LYS PRO GLU SEQRES 14 A 228 LEU LEU LYS LYS GLY PHE GLU LEU VAL LYS SER GLU GLY SEQRES 15 A 228 LEU ALA VAL THR ASP ASP VAL SER ILE VAL GLU TYR LEU SEQRES 16 A 228 LYS HIS PRO VAL TYR VAL SER GLN GLY SER TYR THR ASN SEQRES 17 A 228 ILE LYS VAL THR THR PRO ASP ASP LEU LEU LEU ALA GLU SEQRES 18 A 228 ARG ILE LEU SER GLU ASP SER HET Q9P A 401 18 HET TRS A 402 8 HET ACT A 403 4 HET K A 404 1 HET CD A 405 1 HET CD A 406 1 HET CD A 407 1 HETNAM Q9P AZOLOPYRIMIDINE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM ACT ACETATE ION HETNAM K POTASSIUM ION HETNAM CD CADMIUM ION HETSYN TRS TRIS BUFFER FORMUL 2 Q9P C12 H9 CL N4 O FORMUL 3 TRS C4 H12 N O3 1+ FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 K K 1+ FORMUL 6 CD 3(CD 2+) FORMUL 9 HOH *134(H2 O) HELIX 1 AA1 PRO A 97 TYR A 100 5 4 HELIX 2 AA2 ILE A 108 ARG A 118 1 11 HELIX 3 AA3 ASP A 130 PHE A 132 5 3 HELIX 4 AA4 PHE A 133 GLU A 139 1 7 HELIX 5 AA5 GLU A 156 GLN A 166 1 11 HELIX 6 AA6 ASN A 186 GLY A 201 1 16 HELIX 7 AA7 LYS A 241 GLY A 256 1 16 HELIX 8 AA8 VAL A 263 TYR A 268 1 6 HELIX 9 AA9 THR A 287 SER A 299 1 13 SHEET 1 AA1 7 ASP A 147 ALA A 151 0 SHEET 2 AA1 7 VAL A 122 VAL A 128 1 N VAL A 127 O SER A 149 SHEET 3 AA1 7 VAL A 79 LEU A 84 1 N VAL A 81 O VAL A 126 SHEET 4 AA1 7 LEU A 174 ASP A 179 1 O HIS A 178 N LEU A 84 SHEET 5 AA1 7 TRP A 232 ILE A 240 -1 O ILE A 240 N VAL A 175 SHEET 6 AA1 7 ALA A 202 PRO A 208 -1 N ALA A 203 O VAL A 239 SHEET 7 AA1 7 TYR A 274 GLN A 277 1 O TYR A 274 N ALA A 202 SHEET 1 AA2 2 PRO A 102 LEU A 103 0 SHEET 2 AA2 2 GLN A 106 PRO A 107 -1 O GLN A 106 N LEU A 103 LINK OE1 GLU A 121 CD CD A 407 1555 1555 2.67 LINK OE2 GLU A 121 CD CD A 407 1555 1555 2.15 LINK OE2 GLU A 138 CD CD A 406 1555 4555 2.44 LINK OE1 GLU A 141 CD CD A 406 1555 4555 2.12 LINK OE2 GLU A 141 CD CD A 406 1555 4555 2.68 LINK OE1 GLU A 167 CD CD A 405 1555 1555 2.12 LINK OE2 GLU A 167 CD CD A 405 1555 1555 2.34 LINK OD1 ASP A 169 CD CD A 406 1555 1555 2.39 LINK OE2 GLU A 191 CD CD A 407 1555 1555 2.18 LINK ND1 HIS A 271 CD CD A 407 1555 3565 2.27 LINK OD1 ASP A 290 K K A 404 1555 1555 3.25 LINK OD2 ASP A 290 K K A 404 1555 1555 3.24 LINK O ACT A 403 CD CD A 407 1555 1555 2.51 LINK OXT ACT A 403 CD CD A 407 1555 1555 2.61 LINK CD CD A 405 O HOH A 588 1555 1555 2.15 LINK CD CD A 405 O HOH A 588 1555 4555 2.46 LINK CD CD A 405 O HOH A 612 1555 1555 2.11 LINK CD CD A 406 O HOH A 578 1555 1555 2.40 CISPEP 1 THR A 236 PRO A 237 0 6.56 SITE 1 AC1 13 ARG A 157 ILE A 177 ALA A 203 GLN A 238 SITE 2 AC1 13 VAL A 239 VAL A 259 ASP A 261 ASP A 262 SITE 3 AC1 13 VAL A 263 SER A 264 ILE A 265 VAL A 266 SITE 4 AC1 13 HOH A 536 SITE 1 AC2 4 GLU A 295 HOH A 505 HOH A 529 HOH A 634 SITE 1 AC3 10 PRO A 120 GLU A 121 GLU A 191 LEU A 244 SITE 2 AC3 10 LYS A 247 HIS A 271 CD A 407 HOH A 547 SITE 3 AC3 10 HOH A 548 HOH A 563 SITE 1 AC4 1 ASP A 290 SITE 1 AC5 3 GLU A 167 HOH A 588 HOH A 612 SITE 1 AC6 4 GLU A 138 GLU A 141 ASP A 169 HOH A 578 SITE 1 AC7 4 GLU A 121 GLU A 191 HIS A 271 ACT A 403 CRYST1 74.800 74.800 221.990 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 0.013369 0.007719 0.000000 0.00000 SCALE2 0.000000 0.015437 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004505 0.00000