HEADER TRANSFERASE/TRANSFERASE INHIBITOR 09-JUL-15 5CG6 TITLE NEUTRON CRYSTAL STRUCTURE OF HUMAN FARNESYL PYROPHOSPHATE SYNTHASE IN TITLE 2 COMPLEX WITH RISEDRONATE AND ISOPENTENYL PYROPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FARNESYL PYROPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 74-419; COMPND 5 SYNONYM: FPS,(2E,6E)-FARNESYL DIPHOSPHATE SYNTHASE, COMPND 6 DIMETHYLALLYLTRANSTRANSFERASE,FARNESYL DIPHOSPHATE SYNTHASE, COMPND 7 GERANYLTRANSTRANSFERASE; COMPND 8 EC: 2.5.1.10,2.5.1.1; COMPND 9 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 PRENYL TRANSFERASE, BISPHOSPHONATE, TRANSFERASE-TRANSFERASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION; NEUTRON DIFFRACTION AUTHOR T.YOKOYAMA,M.MIZUGUCHI,A.OSTERMANN,K.KUSAKA,N.NIIMURA,T.E.SCHRADER, AUTHOR 2 I.TANAKA REVDAT 6 12-MAR-25 5CG6 1 REMARK ATOM REVDAT 5 03-APR-24 5CG6 1 REMARK REVDAT 4 20-MAR-24 5CG6 1 REMARK LINK REVDAT 3 16-MAY-18 5CG6 1 REMARK ATOM REVDAT 2 04-OCT-17 5CG6 1 JRNL REMARK HETSYN REVDAT 1 14-OCT-15 5CG6 0 JRNL AUTH T.YOKOYAMA,M.MIZUGUCHI,A.OSTERMANN,K.KUSAKA,N.NIIMURA, JRNL AUTH 2 T.E.SCHRADER,I.TANAKA JRNL TITL PROTONATION STATE AND HYDRATION OF BISPHOSPHONATE BOUND TO JRNL TITL 2 FARNESYL PYROPHOSPHATE SYNTHASE JRNL REF J.MED.CHEM. V. 58 7549 2015 JRNL REFN ISSN 0022-2623 JRNL PMID 26314394 JRNL DOI 10.1021/ACS.JMEDCHEM.5B01147 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 X-RAY DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 49901 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2499 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 0.0000 - 1.7000 0.97 2782 144 0.3860 0.3860 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 6284 REMARK 3 ANGLE : 1.082 11232 REMARK 3 CHIRALITY : 0.183 427 REMARK 3 PLANARITY : 0.005 1253 REMARK 3 DIHEDRAL : 19.852 1813 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 3 NEUTRON DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 18151 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.260 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 904 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 2.5500 - 2.4000 0.00 0 0 0.0000 0.0000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.480 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5CG6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211427. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49965 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 44.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.77700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5CG5 REMARK 200 REMARK 200 REMARK: NULL REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 06-MAR-14 REMARK 230 TEMPERATURE (KELVIN) : 293.0 REMARK 230 PH : NULL REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : NULL REMARK 230 WAVELENGTH OR RANGE (A) : 3.2-6.2 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : IMAGE PLATE REMARK 230 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 230 INTENSITY-INTEGRATION SOFTWARE : STARGAZER REMARK 230 DATA SCALING SOFTWARE : HKL-2000 REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 18171 REMARK 230 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 230 RESOLUTION RANGE LOW (A) : 22.160 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 230 DATA REDUNDANCY : 2.800 REMARK 230 R MERGE (I) : 0.19800 REMARK 230 R SYM (I) : NULL REMARK 230 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 230 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 230 DATA REDUNDANCY IN SHELL : 2.70 REMARK 230 R MERGE FOR SHELL (I) : 0.37900 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 <I/SIGMA(I)> FOR SHELL : NULL REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : MOLREP REMARK 230 STARTING MODEL: 5CG5 REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M NACL, 0.08 M SODIUM ACETATE, REMARK 280 0.02 M ACETIC ACID, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K 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 36.27650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.81350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.81350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.13825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.81350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.81350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.41475 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.81350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.81350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 18.13825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.81350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.81350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.41475 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 36.27650 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: 18310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 -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 -36.27650 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 7 REMARK 465 ARG A 351 REMARK 465 ARG A 352 REMARK 465 LYS A 353 REMARK 465 LEU A 354 REMARK 465 GLU A 355 REMARK 465 HIS A 356 REMARK 465 HIS A 357 REMARK 465 HIS A 358 REMARK 465 HIS A 359 REMARK 465 HIS A 360 REMARK 465 HIS A 361 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 MET A 33 CB CG SD CE REMARK 470 LYS A 350 CB CG CD CE NZ 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 70 CD GLU A 70 OE1 -0.075 REMARK 500 GLU A 70 CD GLU A 70 OE2 0.068 REMARK 500 GLU A 93 CD GLU A 93 OE2 0.072 REMARK 500 GLU A 136 CD GLU A 136 OE1 -0.070 REMARK 500 GLU A 168 CD GLU A 168 OE2 0.072 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 HIS A 35 89.32 -156.48 REMARK 500 GLN A 77 52.45 -105.93 REMARK 500 VAL A 124 -75.51 -98.66 REMARK 500 PHE A 206 -50.74 -125.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 AUTHOR STATES THAT THE PYRIDINE NITROGEN FOR THE LIGAND RIS IS IN REMARK 600 THE PROTONATED FORM IN THE CRYSTAL. IN THE DEPOSITED COORDINATES, REMARK 600 THE LIGAND RIS HAS TWO DEUTERIUMS, RSD AND D13. HETATM 6120 DRS RIS REMARK 600 A 404 13.912 -30.522 -7.556 1.00 17.34 D 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 A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 OD1 REMARK 620 2 ASP A 107 OD2 87.1 REMARK 620 3 RIS A 404 O17 95.6 80.8 REMARK 620 4 DOD A 505 O 93.8 177.2 96.5 REMARK 620 5 DOD A 526 O 87.8 98.7 176.5 84.0 REMARK 620 6 DOD A 539 O 176.2 90.4 86.8 88.8 89.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 OD2 REMARK 620 2 ASP A 107 OD2 86.3 REMARK 620 3 RIS A 404 O12 96.0 172.5 REMARK 620 4 RIS A 404 O17 92.1 78.7 94.1 REMARK 620 5 DOD A 507 O 82.8 94.1 93.2 171.5 REMARK 620 6 DOD A 541 O 169.3 85.4 93.1 92.8 91.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 243 OD2 REMARK 620 2 RIS A 404 O10 95.7 REMARK 620 3 RIS A 404 O15 99.5 97.2 REMARK 620 4 DOD A 514 O 85.0 172.2 90.4 REMARK 620 5 DOD A 517 O 167.0 91.8 90.0 86.2 REMARK 620 6 DOD A 521 O 86.5 80.4 173.7 91.8 84.3 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 MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RIS A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IPE A 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CG5 RELATED DB: PDB DBREF 5CG6 A 8 353 UNP P14324 FPPS_HUMAN 74 419 SEQADV 5CG6 MET A 7 UNP P14324 INITIATING METHIONINE SEQADV 5CG6 LEU A 354 UNP P14324 EXPRESSION TAG SEQADV 5CG6 GLU A 355 UNP P14324 EXPRESSION TAG SEQADV 5CG6 HIS A 356 UNP P14324 EXPRESSION TAG SEQADV 5CG6 HIS A 357 UNP P14324 EXPRESSION TAG SEQADV 5CG6 HIS A 358 UNP P14324 EXPRESSION TAG SEQADV 5CG6 HIS A 359 UNP P14324 EXPRESSION TAG SEQADV 5CG6 HIS A 360 UNP P14324 EXPRESSION TAG SEQADV 5CG6 HIS A 361 UNP P14324 EXPRESSION TAG SEQRES 1 A 355 MET ASP VAL TYR ALA GLN GLU LYS GLN ASP PHE VAL GLN SEQRES 2 A 355 HIS PHE SER GLN ILE VAL ARG VAL LEU THR GLU ASP GLU SEQRES 3 A 355 MET GLY HIS PRO GLU ILE GLY ASP ALA ILE ALA ARG LEU SEQRES 4 A 355 LYS GLU VAL LEU GLU TYR ASN ALA ILE GLY GLY LYS TYR SEQRES 5 A 355 ASN ARG GLY LEU THR VAL VAL VAL ALA PHE ARG GLU LEU SEQRES 6 A 355 VAL GLU PRO ARG LYS GLN ASP ALA ASP SER LEU GLN ARG SEQRES 7 A 355 ALA TRP THR VAL GLY TRP CYS VAL GLU LEU LEU GLN ALA SEQRES 8 A 355 PHE PHE LEU VAL ALA ASP ASP ILE MET ASP SER SER LEU SEQRES 9 A 355 THR ARG ARG GLY GLN ILE CYS TRP TYR GLN LYS PRO GLY SEQRES 10 A 355 VAL GLY LEU ASP ALA ILE ASN ASP ALA ASN LEU LEU GLU SEQRES 11 A 355 ALA CYS ILE TYR ARG LEU LEU LYS LEU TYR CYS ARG GLU SEQRES 12 A 355 GLN PRO TYR TYR LEU ASN LEU ILE GLU LEU PHE LEU GLN SEQRES 13 A 355 SER SER TYR GLN THR GLU ILE GLY GLN THR LEU ASP LEU SEQRES 14 A 355 LEU THR ALA PRO GLN GLY ASN VAL ASP LEU VAL ARG PHE SEQRES 15 A 355 THR GLU LYS ARG TYR LYS SER ILE VAL LYS TYR LYS THR SEQRES 16 A 355 ALA PHE TYR SER PHE TYR LEU PRO ILE ALA ALA ALA MET SEQRES 17 A 355 TYR MET ALA GLY ILE ASP GLY GLU LYS GLU HIS ALA ASN SEQRES 18 A 355 ALA LYS LYS ILE LEU LEU GLU MET GLY GLU PHE PHE GLN SEQRES 19 A 355 ILE GLN ASP ASP TYR LEU ASP LEU PHE GLY ASP PRO SER SEQRES 20 A 355 VAL THR GLY LYS ILE GLY THR ASP ILE GLN ASP ASN LYS SEQRES 21 A 355 CYS SER TRP LEU VAL VAL GLN CYS LEU GLN ARG ALA THR SEQRES 22 A 355 PRO GLU GLN TYR GLN ILE LEU LYS GLU ASN TYR GLY GLN SEQRES 23 A 355 LYS GLU ALA GLU LYS VAL ALA ARG VAL LYS ALA LEU TYR SEQRES 24 A 355 GLU GLU LEU ASP LEU PRO ALA VAL PHE LEU GLN TYR GLU SEQRES 25 A 355 GLU ASP SER TYR SER HIS ILE MET ALA LEU ILE GLU GLN SEQRES 26 A 355 TYR ALA ALA PRO LEU PRO PRO ALA VAL PHE LEU GLY LEU SEQRES 27 A 355 ALA ARG LYS ILE TYR LYS ARG ARG LYS LEU GLU HIS HIS SEQRES 28 A 355 HIS HIS HIS HIS HET MG A 401 1 HET MG A 402 1 HET MG A 403 1 HET RIS A 404 24 HET IPE A 406 23 HETNAM MG MAGNESIUM ION HETNAM RIS 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID HETNAM IPE 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE HETSYN RIS RISEDRONATE HETSYN IPE ISOPENTENYL PYROPHOSPHATE FORMUL 2 MG 3(MG 2+) FORMUL 5 RIS C7 H11 N O7 P2 FORMUL 6 IPE C5 H12 O7 P2 FORMUL 7 DOD *47(D2 O) HELIX 1 AA1 ASP A 8 HIS A 20 1 13 HELIX 2 AA2 HIS A 20 THR A 29 1 10 HELIX 3 AA3 HIS A 35 GLU A 37 5 3 HELIX 4 AA4 ILE A 38 ALA A 53 1 16 HELIX 5 AA5 TYR A 58 VAL A 72 1 15 HELIX 6 AA6 GLU A 73 GLN A 77 5 5 HELIX 7 AA7 ASP A 78 SER A 108 1 31 HELIX 8 AA8 TRP A 118 LYS A 121 5 4 HELIX 9 AA9 VAL A 124 LEU A 126 5 3 HELIX 10 AB1 ASP A 127 ARG A 148 1 22 HELIX 11 AB2 TYR A 152 ALA A 178 1 27 HELIX 12 AB3 ASP A 184 PHE A 188 5 5 HELIX 13 AB4 THR A 189 THR A 201 1 13 HELIX 14 AB5 THR A 201 PHE A 206 1 6 HELIX 15 AB6 PHE A 206 ALA A 217 1 12 HELIX 16 AB7 GLY A 221 GLY A 250 1 30 HELIX 17 AB8 ASP A 251 GLY A 256 1 6 HELIX 18 AB9 SER A 268 ALA A 278 1 11 HELIX 19 AC1 THR A 279 TYR A 290 1 12 HELIX 20 AC2 GLU A 294 LEU A 308 1 15 HELIX 21 AC3 ASP A 309 ALA A 333 1 25 HELIX 22 AC4 PRO A 337 LYS A 350 1 14 SHEET 1 AA1 2 THR A 111 ARG A 112 0 SHEET 2 AA1 2 GLN A 115 ILE A 116 -1 O GLN A 115 N ARG A 112 LINK OD1 ASP A 103 MG MG A 401 1555 1555 2.07 LINK OD2 ASP A 103 MG MG A 402 1555 1555 2.12 LINK OD2 ASP A 107 MG MG A 401 1555 1555 2.13 LINK OD2 ASP A 107 MG MG A 402 1555 1555 2.25 LINK OD2 ASP A 243 MG MG A 403 1555 1555 2.14 LINK MG MG A 401 O17 RIS A 404 1555 1555 2.13 LINK MG MG A 401 O DOD A 505 1555 1555 2.04 LINK MG MG A 401 O DOD A 526 1555 1555 2.10 LINK MG MG A 401 O DOD A 539 1555 1555 2.07 LINK MG MG A 402 O12 RIS A 404 1555 1555 2.04 LINK MG MG A 402 O17 RIS A 404 1555 1555 2.10 LINK MG MG A 402 O DOD A 507 1555 1555 2.06 LINK MG MG A 402 O DOD A 541 1555 1555 2.05 LINK MG MG A 403 O10 RIS A 404 1555 1555 1.93 LINK MG MG A 403 O15 RIS A 404 1555 1555 2.04 LINK MG MG A 403 O DOD A 514 1555 1555 2.09 LINK MG MG A 403 O DOD A 517 1555 1555 2.22 LINK MG MG A 403 O DOD A 521 1555 1555 2.27 CISPEP 1 ALA A 334 PRO A 335 0 5.98 SITE 1 AC1 7 ASP A 103 ASP A 107 MG A 402 RIS A 404 SITE 2 AC1 7 DOD A 505 DOD A 526 DOD A 539 SITE 1 AC2 6 ASP A 103 ASP A 107 MG A 401 RIS A 404 SITE 2 AC2 6 DOD A 507 DOD A 541 SITE 1 AC3 5 ASP A 243 RIS A 404 DOD A 514 DOD A 517 SITE 2 AC3 5 DOD A 521 SITE 1 AC4 22 ASP A 103 ASP A 107 ARG A 112 GLN A 171 SITE 2 AC4 22 LYS A 200 THR A 201 GLN A 240 ASP A 243 SITE 3 AC4 22 LYS A 257 MG A 401 MG A 402 MG A 403 SITE 4 AC4 22 IPE A 406 DOD A 505 DOD A 506 DOD A 507 SITE 5 AC4 22 DOD A 514 DOD A 517 DOD A 521 DOD A 535 SITE 6 AC4 22 DOD A 539 DOD A 541 SITE 1 AC5 13 GLY A 56 LYS A 57 ARG A 60 GLN A 96 SITE 2 AC5 13 ARG A 113 TYR A 204 PHE A 239 ASP A 243 SITE 3 AC5 13 RIS A 404 DOD A 512 DOD A 515 DOD A 518 SITE 4 AC5 13 DOD A 528 CRYST1 111.627 111.627 72.553 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 0.008958 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008958 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013783 0.00000