HEADER TRANSFERASE/TRANSFERASE INHIBITOR 31-OCT-13 4NFI TITLE CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH MAGNESIUM AND JDS05120 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 4NFI 1 REMARK SEQADV LINK REVDAT 2 25-OCT-17 4NFI 1 JRNL REVDAT 1 31-DEC-14 4NFI 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. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 33802 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1781 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2472 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2748 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 205 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.53000 REMARK 3 B22 (A**2) : -2.53000 REMARK 3 B33 (A**2) : 5.06000 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): 0.116 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.111 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.216 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): 2879 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2726 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3913 ; 1.857 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6260 ; 0.984 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 352 ; 5.256 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;34.424 ;24.706 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 493 ;14.818 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;21.613 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 431 ; 0.132 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3281 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 668 ; 0.002 ; 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): 1399 ; 1.675 ; 2.058 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1398 ; 1.671 ; 2.057 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1754 ; 2.266 ; 3.074 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1755 ; 2.266 ; 3.075 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1480 ; 2.593 ; 2.374 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1481 ; 2.592 ; 2.375 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2157 ; 3.894 ; 3.448 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3627 ; 6.305 ;18.224 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3540 ; 6.236 ;17.707 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 : 5 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 35 REMARK 3 ORIGIN FOR THE GROUP (A): 0.2533 28.1000 9.6543 REMARK 3 T TENSOR REMARK 3 T11: 0.1853 T22: 0.3427 REMARK 3 T33: 0.1554 T12: 0.0405 REMARK 3 T13: 0.0872 T23: -0.0334 REMARK 3 L TENSOR REMARK 3 L11: 7.7504 L22: 7.5637 REMARK 3 L33: 6.0106 L12: -4.3431 REMARK 3 L13: 4.5155 L23: -3.5185 REMARK 3 S TENSOR REMARK 3 S11: -0.1538 S12: -0.6007 S13: -0.0047 REMARK 3 S21: 0.3313 S22: 0.3103 S23: 0.2703 REMARK 3 S31: -0.4125 S32: -0.5284 S33: -0.1565 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 36 F 137 REMARK 3 ORIGIN FOR THE GROUP (A): 9.0981 27.5878 4.5289 REMARK 3 T TENSOR REMARK 3 T11: 0.0664 T22: 0.1244 REMARK 3 T33: 0.0845 T12: 0.0146 REMARK 3 T13: 0.0272 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 1.6223 L22: 1.3241 REMARK 3 L33: 1.4592 L12: 0.5447 REMARK 3 L13: 0.5479 L23: -0.0813 REMARK 3 S TENSOR REMARK 3 S11: 0.0081 S12: -0.3757 S13: 0.2207 REMARK 3 S21: 0.1612 S22: 0.0098 S23: 0.3173 REMARK 3 S31: -0.0577 S32: -0.3163 S33: -0.0179 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 138 F 196 REMARK 3 ORIGIN FOR THE GROUP (A): 13.0535 21.0186 -8.6843 REMARK 3 T TENSOR REMARK 3 T11: 0.0484 T22: 0.0285 REMARK 3 T33: 0.0345 T12: 0.0221 REMARK 3 T13: -0.0339 T23: -0.0194 REMARK 3 L TENSOR REMARK 3 L11: 3.5565 L22: 3.4675 REMARK 3 L33: 4.4364 L12: 1.4703 REMARK 3 L13: -1.6078 L23: -2.3557 REMARK 3 S TENSOR REMARK 3 S11: 0.0074 S12: 0.0008 S13: -0.1921 REMARK 3 S21: -0.1963 S22: 0.0088 S23: 0.0401 REMARK 3 S31: 0.0988 S32: 0.1761 S33: -0.0162 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 197 F 324 REMARK 3 ORIGIN FOR THE GROUP (A): 12.0342 36.3852 -17.0817 REMARK 3 T TENSOR REMARK 3 T11: 0.1119 T22: 0.0902 REMARK 3 T33: 0.0528 T12: 0.0060 REMARK 3 T13: -0.0383 T23: 0.0302 REMARK 3 L TENSOR REMARK 3 L11: 2.7479 L22: 1.5975 REMARK 3 L33: 0.9020 L12: 0.5785 REMARK 3 L13: 0.1199 L23: -0.2161 REMARK 3 S TENSOR REMARK 3 S11: -0.0543 S12: 0.3234 S13: 0.3144 REMARK 3 S21: -0.2652 S22: 0.0899 S23: 0.1808 REMARK 3 S31: -0.1023 S32: 0.0336 S33: -0.0356 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 325 F 353 REMARK 3 ORIGIN FOR THE GROUP (A): -5.7125 30.3004 -14.8709 REMARK 3 T TENSOR REMARK 3 T11: 0.0958 T22: 0.1320 REMARK 3 T33: 0.1328 T12: 0.0260 REMARK 3 T13: -0.0698 T23: 0.0260 REMARK 3 L TENSOR REMARK 3 L11: 3.6545 L22: 3.7374 REMARK 3 L33: 5.3022 L12: -0.0797 REMARK 3 L13: -0.4686 L23: 0.7353 REMARK 3 S TENSOR REMARK 3 S11: 0.0466 S12: -0.0911 S13: 0.2067 REMARK 3 S21: 0.1285 S22: 0.0803 S23: 0.0225 REMARK 3 S31: -0.3185 S32: -0.0248 S33: -0.1270 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 4NFI 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_1000083137. 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 : 5.9 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35614 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 0.43700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.980 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 (%): 48.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2M MAGNESIUM FORMATE, REMARK 280 PH 5.9, VAPOR 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 33.48500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.25500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.25500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.74250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.25500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.25500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 50.22750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.25500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.25500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 16.74250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.25500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.25500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.22750 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 33.48500 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: 4670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.0 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 ASP F 31 REMARK 465 GLU F 32 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 GLU F 30 CG CD OE1 OE2 REMARK 470 MET F 33 CG SD CE REMARK 470 LYS F 57 CE NZ REMARK 470 LYS F 76 CE NZ REMARK 470 GLN F 180 CG CD OE1 NE2 REMARK 470 GLU F 222 CD OE1 OE2 REMARK 470 LYS F 223 CD CE NZ REMARK 470 ARG F 346 CD NE CZ NH1 NH2 REMARK 470 ARG F 351 CG CD NE CZ NH1 NH2 REMARK 470 ARG F 352 CG CD NE CZ NH1 NH2 REMARK 470 LYS F 353 CE NZ 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 O HOH F 642 O HOH F 657 2.16 REMARK 500 O HOH F 603 O HOH F 680 2.16 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 GLY F 55 N GLY F 55 CA 0.095 REMARK 500 GLU F 136 CD GLU F 136 OE2 0.071 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG F 192 NE - CZ - NH1 ANGL. DEV. = -3.3 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 GLN F 77 56.86 -104.65 REMARK 500 VAL F 124 -71.28 -100.05 REMARK 500 THR F 201 -43.49 -131.86 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 84.0 REMARK 620 3 JD5 F 401 OAK 101.2 82.5 REMARK 620 4 HOH F 502 O 88.9 98.4 169.9 REMARK 620 5 HOH F 503 O 173.3 96.1 85.4 84.5 REMARK 620 6 HOH F 505 O 89.5 172.0 94.4 86.0 90.9 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 89.8 REMARK 620 3 JD5 F 401 OAP 90.0 172.3 REMARK 620 4 JD5 F 401 OAK 93.4 77.5 94.8 REMARK 620 5 HOH F 506 O 167.7 85.7 95.9 96.8 REMARK 620 6 HOH F 509 O 81.2 95.8 91.8 171.5 87.9 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 103.5 REMARK 620 3 JD5 F 401 OAO 95.9 94.9 REMARK 620 4 HOH F 501 O 163.9 87.4 94.8 REMARK 620 5 HOH F 504 O 82.8 88.4 176.7 85.9 REMARK 620 6 HOH F 508 O 85.7 170.5 86.6 83.0 90.3 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NFJ RELATED DB: PDB REMARK 900 RELATED ID: 4NFK RELATED DB: PDB DBREF 4NFI F 1 353 UNP P14324 FPPS_HUMAN 67 419 SEQADV 4NFI MET F -21 UNP P14324 EXPRESSION TAG SEQADV 4NFI GLY F -20 UNP P14324 EXPRESSION TAG SEQADV 4NFI SER F -19 UNP P14324 EXPRESSION TAG SEQADV 4NFI SER F -18 UNP P14324 EXPRESSION TAG SEQADV 4NFI HIS F -17 UNP P14324 EXPRESSION TAG SEQADV 4NFI HIS F -16 UNP P14324 EXPRESSION TAG SEQADV 4NFI HIS F -15 UNP P14324 EXPRESSION TAG SEQADV 4NFI HIS F -14 UNP P14324 EXPRESSION TAG SEQADV 4NFI HIS F -13 UNP P14324 EXPRESSION TAG SEQADV 4NFI HIS F -12 UNP P14324 EXPRESSION TAG SEQADV 4NFI SER F -11 UNP P14324 EXPRESSION TAG SEQADV 4NFI SER F -10 UNP P14324 EXPRESSION TAG SEQADV 4NFI GLY F -9 UNP P14324 EXPRESSION TAG SEQADV 4NFI ARG F -8 UNP P14324 EXPRESSION TAG SEQADV 4NFI GLU F -7 UNP P14324 EXPRESSION TAG SEQADV 4NFI ASN F -6 UNP P14324 EXPRESSION TAG SEQADV 4NFI LEU F -5 UNP P14324 EXPRESSION TAG SEQADV 4NFI TYR F -4 UNP P14324 EXPRESSION TAG SEQADV 4NFI PHE F -3 UNP P14324 EXPRESSION TAG SEQADV 4NFI GLN F -2 UNP P14324 EXPRESSION TAG SEQADV 4NFI GLY F -1 UNP P14324 EXPRESSION TAG SEQADV 4NFI 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 HETNAM JD5 [({5-[4-(CYCLOPROPYLOXY)PHENYL]PYRIDIN-3-YL}AMINO) HETNAM 2 JD5 METHANEDIYL]BIS(PHOSPHONIC ACID) HETNAM MG MAGNESIUM ION FORMUL 2 JD5 C15 H18 N2 O7 P2 FORMUL 3 MG 3(MG 2+) FORMUL 6 HOH *205(H2 O) HELIX 1 1 ASP F 8 THR F 29 1 22 HELIX 2 2 HIS F 35 GLU F 37 5 3 HELIX 3 3 ILE F 38 ALA F 53 1 16 HELIX 4 4 TYR F 58 VAL F 72 1 15 HELIX 5 5 GLU F 73 GLN F 77 5 5 HELIX 6 6 ASP F 78 ASP F 107 1 30 HELIX 7 7 TRP F 118 LYS F 121 5 4 HELIX 8 8 VAL F 124 LEU F 126 5 3 HELIX 9 9 ASP F 127 ARG F 148 1 22 HELIX 10 10 TYR F 152 ALA F 178 1 27 HELIX 11 11 ASP F 184 PHE F 188 5 5 HELIX 12 12 THR F 189 THR F 201 1 13 HELIX 13 13 THR F 201 PHE F 206 1 6 HELIX 14 14 PHE F 206 ALA F 217 1 12 HELIX 15 15 GLY F 221 GLY F 250 1 30 HELIX 16 16 ASP F 251 GLY F 256 1 6 HELIX 17 17 SER F 268 ALA F 278 1 11 HELIX 18 18 THR F 279 TYR F 290 1 12 HELIX 19 19 GLU F 294 LEU F 308 1 15 HELIX 20 20 ASP F 309 ALA F 333 1 25 HELIX 21 21 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 2.13 LINK OD1 ASP F 103 MG MG F 404 1555 1555 2.07 LINK OD2 ASP F 107 MG MG F 402 1555 1555 2.07 LINK OD2 ASP F 107 MG MG F 404 1555 1555 2.17 LINK OD2 ASP F 243 MG MG F 403 1555 1555 2.11 LINK OAK JD5 F 401 MG MG F 402 1555 1555 2.01 LINK OAL JD5 F 401 MG MG F 403 1555 1555 1.97 LINK OAO JD5 F 401 MG MG F 403 1555 1555 1.99 LINK OAP JD5 F 401 MG MG F 404 1555 1555 2.06 LINK OAK JD5 F 401 MG MG F 404 1555 1555 2.13 LINK MG MG F 402 O HOH F 502 1555 1555 2.06 LINK MG MG F 402 O HOH F 503 1555 1555 2.18 LINK MG MG F 402 O HOH F 505 1555 1555 2.02 LINK MG MG F 403 O HOH F 501 1555 1555 2.12 LINK MG MG F 403 O HOH F 504 1555 1555 2.12 LINK MG MG F 403 O HOH F 508 1555 1555 2.20 LINK MG MG F 404 O HOH F 506 1555 1555 2.05 LINK MG MG F 404 O HOH F 509 1555 1555 2.19 CISPEP 1 ALA F 334 PRO F 335 0 12.43 SITE 1 AC1 29 PHE F 98 PHE F 99 ALA F 102 ASP F 103 SITE 2 AC1 29 MET F 106 ASP F 107 ARG F 112 ASN F 130 SITE 3 AC1 29 ASN F 133 THR F 167 GLN F 171 LYS F 200 SITE 4 AC1 29 THR F 201 ASP F 243 LYS F 257 MG F 402 SITE 5 AC1 29 MG F 403 MG F 404 HOH F 501 HOH F 503 SITE 6 AC1 29 HOH F 504 HOH F 505 HOH F 506 HOH F 507 SITE 7 AC1 29 HOH F 508 HOH F 509 HOH F 520 HOH F 539 SITE 8 AC1 29 HOH F 581 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 508 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 509 CRYST1 110.510 110.510 66.970 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 0.009049 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009049 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014932 0.00000