HEADER TRANSFERASE/TRANSFERASE INHIBITOR 31-OCT-13 4NFJ TITLE CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH MAGNESIUM, JDS05120, TITLE 2 AND SULFATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FARNESYL PYROPHOSPHATE SYNTHASE; COMPND 3 CHAIN: F; COMPND 4 SYNONYM: FPP SYNTHASE, FPS, (2E,6E)-FARNESYL DIPHOSPHATE SYNTHASE, COMPND 5 DIMETHYLALLYLTRANSTRANSFERASE, FARNESYL DIPHOSPHATE SYNTHASE, COMPND 6 GERANYLTRANSTRANSFERASE; COMPND 7 EC: 2.5.1.10, 2.5.1.1; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FDPS, FPS, KIAA1293; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.PARK,J.W.DE SCHUTTER,Y.S.TSANTRIZOS,A.M.BERGHUIS REVDAT 3 20-SEP-23 4NFJ 1 REMARK SEQADV LINK REVDAT 2 25-OCT-17 4NFJ 1 JRNL REVDAT 1 31-DEC-14 4NFJ 0 JRNL AUTH J.PARK,D.RODIONOV,J.W.DE SCHUTTER,Y.S.LIN,Y.S.TSANTRIZOS, JRNL AUTH 2 A.M.BERGHUIS JRNL TITL CRYSTALLOGRAPHIC AND THERMODYNAMIC CHARACTERIZATION OF JRNL TITL 2 PHENYLAMINOPYRIDINE BISPHOSPHONATES BINDING TO HUMAN JRNL TITL 3 FARNESYL PYROPHOSPHATE SYNTHASE. JRNL REF PLOS ONE V. 12 86447 2017 JRNL REFN ESSN 1932-6203 JRNL PMID 29036218 JRNL DOI 10.1371/JOURNAL.PONE.0186447 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 25777 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1360 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1851 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2709 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 105 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.70000 REMARK 3 B22 (A**2) : -2.70000 REMARK 3 B33 (A**2) : 5.39000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.161 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.148 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.680 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2800 ; 0.018 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2608 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3809 ; 1.891 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5976 ; 0.950 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 342 ; 5.393 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 131 ;37.057 ;24.809 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 458 ;14.949 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.770 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 424 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3185 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 646 ; 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): 1371 ; 2.078 ; 2.866 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1370 ; 2.071 ; 2.864 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1712 ; 2.805 ; 4.284 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1713 ; 2.804 ; 4.286 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1429 ; 3.075 ; 3.242 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1426 ; 3.074 ; 3.241 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2089 ; 4.642 ; 4.739 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3408 ; 6.274 ;24.518 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3372 ; 6.274 ;24.316 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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 : F 8 F 33 REMARK 3 ORIGIN FOR THE GROUP (A): 0.5543 28.2939 9.4729 REMARK 3 T TENSOR REMARK 3 T11: 0.1534 T22: 0.3488 REMARK 3 T33: 0.2037 T12: 0.0613 REMARK 3 T13: 0.0759 T23: -0.0738 REMARK 3 L TENSOR REMARK 3 L11: 6.1033 L22: 5.2320 REMARK 3 L33: 10.4974 L12: -2.3284 REMARK 3 L13: 3.8879 L23: -2.6860 REMARK 3 S TENSOR REMARK 3 S11: -0.0106 S12: -0.6461 S13: -0.2612 REMARK 3 S21: 0.2285 S22: 0.3684 S23: 0.5249 REMARK 3 S31: -0.2385 S32: -0.8329 S33: -0.3579 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 34 F 140 REMARK 3 ORIGIN FOR THE GROUP (A): 9.4849 27.2704 4.7804 REMARK 3 T TENSOR REMARK 3 T11: 0.0408 T22: 0.0964 REMARK 3 T33: 0.0385 T12: 0.0413 REMARK 3 T13: 0.0224 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 3.1531 L22: 2.0687 REMARK 3 L33: 1.7273 L12: 0.1733 REMARK 3 L13: 1.0471 L23: 0.1628 REMARK 3 S TENSOR REMARK 3 S11: 0.0109 S12: -0.3829 S13: 0.1675 REMARK 3 S21: 0.1297 S22: 0.0547 S23: 0.1914 REMARK 3 S31: -0.1358 S32: -0.3124 S33: -0.0656 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 141 F 315 REMARK 3 ORIGIN FOR THE GROUP (A): 13.2542 31.6441 -14.3046 REMARK 3 T TENSOR REMARK 3 T11: 0.0768 T22: 0.1174 REMARK 3 T33: 0.0470 T12: 0.0182 REMARK 3 T13: -0.0422 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 2.2791 L22: 2.8748 REMARK 3 L33: 1.5589 L12: 0.9883 REMARK 3 L13: -0.5132 L23: -1.0294 REMARK 3 S TENSOR REMARK 3 S11: -0.0756 S12: 0.1648 S13: 0.1895 REMARK 3 S21: -0.2666 S22: 0.0910 S23: 0.0767 REMARK 3 S31: -0.0389 S32: 0.0849 S33: -0.0154 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 316 F 350 REMARK 3 ORIGIN FOR THE GROUP (A): -4.7296 31.6251 -17.5126 REMARK 3 T TENSOR REMARK 3 T11: 0.0874 T22: 0.1779 REMARK 3 T33: 0.1807 T12: 0.0145 REMARK 3 T13: -0.0941 T23: 0.0321 REMARK 3 L TENSOR REMARK 3 L11: 2.9121 L22: 3.9621 REMARK 3 L33: 3.8765 L12: 0.9010 REMARK 3 L13: -1.0769 L23: -1.6967 REMARK 3 S TENSOR REMARK 3 S11: 0.0739 S12: 0.0094 S13: 0.3019 REMARK 3 S21: -0.0008 S22: 0.0430 S23: 0.3690 REMARK 3 S31: -0.1185 S32: -0.0887 S33: -0.1169 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 4NFJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000083138. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : ACCEL/BRUKER DCM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27177 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 9.30 REMARK 200 R MERGE FOR SHELL (I) : 0.47200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.8.0049 REMARK 200 STARTING MODEL: PDB ENTRY 4DEM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25.5% PEG MME 2000, 0.17M AMMONIUM REMARK 280 SULFATE, 15% GLYCEROL, 0.09M SODIUM ACETATE, PH 4.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.95950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.61750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.61750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.97975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.61750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.61750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 50.93925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.61750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.61750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 16.97975 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.61750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.61750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.93925 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 33.95950 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: 5080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -114.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F 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 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 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 MET F -21 REMARK 465 GLY F -20 REMARK 465 SER F -19 REMARK 465 SER F -18 REMARK 465 HIS F -17 REMARK 465 HIS F -16 REMARK 465 HIS F -15 REMARK 465 HIS F -14 REMARK 465 HIS F -13 REMARK 465 HIS F -12 REMARK 465 SER F -11 REMARK 465 SER F -10 REMARK 465 GLY F -9 REMARK 465 ARG F -8 REMARK 465 GLU F -7 REMARK 465 ASN F -6 REMARK 465 LEU F -5 REMARK 465 TYR F -4 REMARK 465 PHE F -3 REMARK 465 GLN F -2 REMARK 465 GLY F -1 REMARK 465 HIS F 0 REMARK 465 MET F 1 REMARK 465 ASN F 2 REMARK 465 GLY F 3 REMARK 465 ASP F 4 REMARK 465 GLN F 5 REMARK 465 ASN F 6 REMARK 465 SER F 7 REMARK 465 ARG F 351 REMARK 465 ARG F 352 REMARK 465 LYS F 353 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 GLN F 15 CG CD OE1 NE2 REMARK 470 GLU F 30 CG CD OE1 OE2 REMARK 470 MET F 33 CG SD CE REMARK 470 LYS F 57 CD CE NZ REMARK 470 LYS F 76 CE NZ REMARK 470 LYS F 121 CE NZ REMARK 470 ARG F 148 CG CD NE CZ NH1 NH2 REMARK 470 GLU F 149 CD OE1 OE2 REMARK 470 GLN F 180 CG CD OE1 NE2 REMARK 470 ASP F 184 CG OD1 OD2 REMARK 470 LYS F 191 CE NZ REMARK 470 GLU F 222 CD OE1 OE2 REMARK 470 LYS F 223 CD CE NZ REMARK 470 LYS F 230 NZ REMARK 470 GLU F 288 CD OE1 OE2 REMARK 470 LYS F 293 NZ REMARK 470 ARG F 300 CD NE CZ NH1 NH2 REMARK 470 LEU F 315 CG CD1 CD2 REMARK 470 ARG F 346 NE CZ NH1 NH2 REMARK 470 LYS F 347 CE NZ REMARK 470 LYS F 350 CG CD CE NZ 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 F 192 NE - CZ - NH1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG F 192 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ASP F 251 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP F 251 CB - CG - OD2 ANGL. DEV. = -6.7 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 F 31 -25.12 -39.25 REMARK 500 VAL F 124 -77.46 -97.24 REMARK 500 VAL F 183 101.68 -47.21 REMARK 500 PHE F 206 -52.08 -126.99 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 MG F 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 103 OD2 REMARK 620 2 ASP F 107 OD2 74.7 REMARK 620 3 JD5 F 401 OAK 104.0 79.7 REMARK 620 4 HOH F 502 O 84.5 90.2 164.4 REMARK 620 5 HOH F 503 O 164.4 93.2 83.1 85.7 REMARK 620 6 HOH F 505 O 102.1 176.0 98.9 91.9 90.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG F 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 103 OD1 REMARK 620 2 ASP F 107 OD2 93.0 REMARK 620 3 JD5 F 401 OAK 106.6 84.2 REMARK 620 4 JD5 F 401 OAP 93.7 173.3 93.5 REMARK 620 5 HOH F 506 O 159.9 82.3 92.4 91.5 REMARK 620 6 HOH F 508 O 77.3 88.5 171.9 93.3 83.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG F 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 243 OD2 REMARK 620 2 JD5 F 401 OAL 98.4 REMARK 620 3 JD5 F 401 OAO 95.3 92.5 REMARK 620 4 HOH F 501 O 173.3 85.3 90.1 REMARK 620 5 HOH F 504 O 89.0 87.3 175.7 85.7 REMARK 620 6 HOH F 507 O 85.8 175.5 85.6 90.6 94.3 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 JD5 F 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 F 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NFI RELATED DB: PDB REMARK 900 RELATED ID: 4NFK RELATED DB: PDB DBREF 4NFJ F 1 353 UNP P14324 FPPS_HUMAN 67 419 SEQADV 4NFJ MET F -21 UNP P14324 EXPRESSION TAG SEQADV 4NFJ GLY F -20 UNP P14324 EXPRESSION TAG SEQADV 4NFJ SER F -19 UNP P14324 EXPRESSION TAG SEQADV 4NFJ SER F -18 UNP P14324 EXPRESSION TAG SEQADV 4NFJ HIS F -17 UNP P14324 EXPRESSION TAG SEQADV 4NFJ HIS F -16 UNP P14324 EXPRESSION TAG SEQADV 4NFJ HIS F -15 UNP P14324 EXPRESSION TAG SEQADV 4NFJ HIS F -14 UNP P14324 EXPRESSION TAG SEQADV 4NFJ HIS F -13 UNP P14324 EXPRESSION TAG SEQADV 4NFJ HIS F -12 UNP P14324 EXPRESSION TAG SEQADV 4NFJ SER F -11 UNP P14324 EXPRESSION TAG SEQADV 4NFJ SER F -10 UNP P14324 EXPRESSION TAG SEQADV 4NFJ GLY F -9 UNP P14324 EXPRESSION TAG SEQADV 4NFJ ARG F -8 UNP P14324 EXPRESSION TAG SEQADV 4NFJ GLU F -7 UNP P14324 EXPRESSION TAG SEQADV 4NFJ ASN F -6 UNP P14324 EXPRESSION TAG SEQADV 4NFJ LEU F -5 UNP P14324 EXPRESSION TAG SEQADV 4NFJ TYR F -4 UNP P14324 EXPRESSION TAG SEQADV 4NFJ PHE F -3 UNP P14324 EXPRESSION TAG SEQADV 4NFJ GLN F -2 UNP P14324 EXPRESSION TAG SEQADV 4NFJ GLY F -1 UNP P14324 EXPRESSION TAG SEQADV 4NFJ HIS F 0 UNP P14324 EXPRESSION TAG SEQRES 1 F 375 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 F 375 ARG GLU ASN LEU TYR PHE GLN GLY HIS MET ASN GLY ASP SEQRES 3 F 375 GLN ASN SER ASP VAL TYR ALA GLN GLU LYS GLN ASP PHE SEQRES 4 F 375 VAL GLN HIS PHE SER GLN ILE VAL ARG VAL LEU THR GLU SEQRES 5 F 375 ASP GLU MET GLY HIS PRO GLU ILE GLY ASP ALA ILE ALA SEQRES 6 F 375 ARG LEU LYS GLU VAL LEU GLU TYR ASN ALA ILE GLY GLY SEQRES 7 F 375 LYS TYR ASN ARG GLY LEU THR VAL VAL VAL ALA PHE ARG SEQRES 8 F 375 GLU LEU VAL GLU PRO ARG LYS GLN ASP ALA ASP SER LEU SEQRES 9 F 375 GLN ARG ALA TRP THR VAL GLY TRP CYS VAL GLU LEU LEU SEQRES 10 F 375 GLN ALA PHE PHE LEU VAL ALA ASP ASP ILE MET ASP SER SEQRES 11 F 375 SER LEU THR ARG ARG GLY GLN ILE CYS TRP TYR GLN LYS SEQRES 12 F 375 PRO GLY VAL GLY LEU ASP ALA ILE ASN ASP ALA ASN LEU SEQRES 13 F 375 LEU GLU ALA CYS ILE TYR ARG LEU LEU LYS LEU TYR CYS SEQRES 14 F 375 ARG GLU GLN PRO TYR TYR LEU ASN LEU ILE GLU LEU PHE SEQRES 15 F 375 LEU GLN SER SER TYR GLN THR GLU ILE GLY GLN THR LEU SEQRES 16 F 375 ASP LEU LEU THR ALA PRO GLN GLY ASN VAL ASP LEU VAL SEQRES 17 F 375 ARG PHE THR GLU LYS ARG TYR LYS SER ILE VAL LYS TYR SEQRES 18 F 375 LYS THR ALA PHE TYR SER PHE TYR LEU PRO ILE ALA ALA SEQRES 19 F 375 ALA MET TYR MET ALA GLY ILE ASP GLY GLU LYS GLU HIS SEQRES 20 F 375 ALA ASN ALA LYS LYS ILE LEU LEU GLU MET GLY GLU PHE SEQRES 21 F 375 PHE GLN ILE GLN ASP ASP TYR LEU ASP LEU PHE GLY ASP SEQRES 22 F 375 PRO SER VAL THR GLY LYS ILE GLY THR ASP ILE GLN ASP SEQRES 23 F 375 ASN LYS CYS SER TRP LEU VAL VAL GLN CYS LEU GLN ARG SEQRES 24 F 375 ALA THR PRO GLU GLN TYR GLN ILE LEU LYS GLU ASN TYR SEQRES 25 F 375 GLY GLN LYS GLU ALA GLU LYS VAL ALA ARG VAL LYS ALA SEQRES 26 F 375 LEU TYR GLU GLU LEU ASP LEU PRO ALA VAL PHE LEU GLN SEQRES 27 F 375 TYR GLU GLU ASP SER TYR SER HIS ILE MET ALA LEU ILE SEQRES 28 F 375 GLU GLN TYR ALA ALA PRO LEU PRO PRO ALA VAL PHE LEU SEQRES 29 F 375 GLY LEU ALA ARG LYS ILE TYR LYS ARG ARG LYS HET JD5 F 401 26 HET MG F 402 1 HET MG F 403 1 HET MG F 404 1 HET SO4 F 405 5 HETNAM JD5 [({5-[4-(CYCLOPROPYLOXY)PHENYL]PYRIDIN-3-YL}AMINO) HETNAM 2 JD5 METHANEDIYL]BIS(PHOSPHONIC ACID) HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION FORMUL 2 JD5 C15 H18 N2 O7 P2 FORMUL 3 MG 3(MG 2+) FORMUL 6 SO4 O4 S 2- FORMUL 7 HOH *105(H2 O) HELIX 1 1 ASP F 8 HIS F 20 1 13 HELIX 2 2 HIS F 20 ASP F 31 1 12 HELIX 3 3 HIS F 35 GLU F 37 5 3 HELIX 4 4 ILE F 38 ALA F 53 1 16 HELIX 5 5 TYR F 58 VAL F 72 1 15 HELIX 6 6 GLU F 73 GLN F 77 5 5 HELIX 7 7 ASP F 78 ASP F 107 1 30 HELIX 8 8 TRP F 118 LYS F 121 5 4 HELIX 9 9 VAL F 124 LEU F 126 5 3 HELIX 10 10 ASP F 127 ARG F 148 1 22 HELIX 11 11 TYR F 152 ALA F 178 1 27 HELIX 12 12 ASP F 184 PHE F 188 5 5 HELIX 13 13 THR F 189 THR F 201 1 13 HELIX 14 14 THR F 201 PHE F 206 1 6 HELIX 15 15 PHE F 206 ALA F 217 1 12 HELIX 16 16 GLY F 221 GLY F 250 1 30 HELIX 17 17 ASP F 251 GLY F 256 1 6 HELIX 18 18 SER F 268 ALA F 278 1 11 HELIX 19 19 THR F 279 TYR F 290 1 12 HELIX 20 20 GLU F 294 LEU F 308 1 15 HELIX 21 21 ASP F 309 ALA F 333 1 25 HELIX 22 22 PRO F 337 TYR F 349 1 13 SHEET 1 A 2 THR F 111 ARG F 112 0 SHEET 2 A 2 GLN F 115 ILE F 116 -1 O GLN F 115 N ARG F 112 LINK OD2 ASP F 103 MG MG F 402 1555 1555 2.33 LINK OD1 ASP F 103 MG MG F 404 1555 1555 2.16 LINK OD2 ASP F 107 MG MG F 402 1555 1555 2.36 LINK OD2 ASP F 107 MG MG F 404 1555 1555 2.26 LINK OD2 ASP F 243 MG MG F 403 1555 1555 2.12 LINK OAK JD5 F 401 MG MG F 402 1555 1555 2.22 LINK OAL JD5 F 401 MG MG F 403 1555 1555 1.96 LINK OAO JD5 F 401 MG MG F 403 1555 1555 1.97 LINK OAK JD5 F 401 MG MG F 404 1555 1555 2.13 LINK OAP JD5 F 401 MG MG F 404 1555 1555 2.15 LINK MG MG F 402 O HOH F 502 1555 1555 2.22 LINK MG MG F 402 O HOH F 503 1555 1555 2.27 LINK MG MG F 402 O HOH F 505 1555 1555 2.14 LINK MG MG F 403 O HOH F 501 1555 1555 2.19 LINK MG MG F 403 O HOH F 504 1555 1555 2.19 LINK MG MG F 403 O HOH F 507 1555 1555 2.16 LINK MG MG F 404 O HOH F 506 1555 1555 2.19 LINK MG MG F 404 O HOH F 508 1555 1555 2.22 CISPEP 1 ALA F 334 PRO F 335 0 10.38 SITE 1 AC1 25 PHE F 99 ASP F 103 MET F 106 ASP F 107 SITE 2 AC1 25 ARG F 112 ASN F 130 ASN F 133 THR F 167 SITE 3 AC1 25 GLU F 168 GLN F 171 LYS F 200 THR F 201 SITE 4 AC1 25 GLN F 240 ASP F 243 LYS F 257 MG F 402 SITE 5 AC1 25 MG F 403 MG F 404 HOH F 501 HOH F 503 SITE 6 AC1 25 HOH F 504 HOH F 505 HOH F 507 HOH F 551 SITE 7 AC1 25 HOH F 563 SITE 1 AC2 7 ASP F 103 ASP F 107 JD5 F 401 MG F 404 SITE 2 AC2 7 HOH F 502 HOH F 503 HOH F 505 SITE 1 AC3 5 ASP F 243 JD5 F 401 HOH F 501 HOH F 504 SITE 2 AC3 5 HOH F 507 SITE 1 AC4 6 ASP F 103 ASP F 107 JD5 F 401 MG F 402 SITE 2 AC4 6 HOH F 506 HOH F 508 SITE 1 AC5 9 GLY F 56 LYS F 57 ARG F 60 GLN F 96 SITE 2 AC5 9 ARG F 113 HOH F 518 HOH F 519 HOH F 545 SITE 3 AC5 9 HOH F 592 CRYST1 111.235 111.235 67.919 90.00 90.00 90.00 P 41 21 2 8 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 0.008990 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008990 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014723 0.00000