PDB Short entry for 5CG5 HEADER TRANSFERASE/TRANSFERASE INHIBOTOR 09-JUL-15 5CG5 TITLE NEUTRON CRYSTAL STRUCTURE OF HUMAN FARNESYL PYROPHOSPHATE SYNTHASE IN TITLE 2 COMPLEX WITH RISEDRONATE 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, BISPHOPHONATE, OSTEOPROSIS, INHIBITOR, KEYWDS 2 TRANSFERASE-TRANSFERASE INHIBOTOR 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 4 03-APR-24 5CG5 1 REMARK REVDAT 3 20-MAR-24 5CG5 1 REMARK LINK ATOM REVDAT 2 04-OCT-17 5CG5 1 JRNL REMARK HETSYN REVDAT 1 14-OCT-15 5CG5 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. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 87160 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 4389 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 1.4200 - 1.4000 0.93 2632 133 0.4908 0.2934 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.350 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 : 0.006 6343 REMARK 3 ANGLE : 0.919 11277 REMARK 3 CHIRALITY : 0.139 424 REMARK 3 PLANARITY : 0.004 1276 REMARK 3 DIHEDRAL : 18.782 1794 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) : 53.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 18386 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 902 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 0.98 2823 165 0.2488 0.2919 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.790 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 5CG5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211426. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 5.00 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 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 87200 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.06200 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) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.48200 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: 1YV5 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-NOV-13 REMARK 230 TEMPERATURE (KELVIN) : 293.0 REMARK 230 PH : 5.00 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : SPALLATION SOURCE REMARK 230 BEAMLINE : BL-03 REMARK 230 WAVELENGTH OR RANGE (A) : 3.99 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : OSCILLATION CAMERA REMARK 230 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 230 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 230 DATA SCALING SOFTWARE : SCALEPACK REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 18415 REMARK 230 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 230 RESOLUTION RANGE LOW (A) : 53.570 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 230 DATA REDUNDANCY : 3.800 REMARK 230 R MERGE (I) : 0.10700 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 (%) : 98.0 REMARK 230 DATA REDUNDANCY IN SHELL : 2.70 REMARK 230 R MERGE FOR SHELL (I) : 0.61200 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: 1YV5 REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5M NACL, 0.1M ACETATE BUFFER, PH REMARK 280 5.00, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 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 36.37700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.98300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.98300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.18850 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.98300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.98300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.56550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.98300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.98300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 18.18850 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.98300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.98300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.56550 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 36.37700 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: 6260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -85.0 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 -36.37700 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: 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 DOD A 569 O DOD A 593 8554 1.88 REMARK 500 OE2 GLU A 330 O DOD A 568 3445 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 70 CD GLU A 70 OE1 -0.071 REMARK 500 GLU A 168 CD GLU A 168 OE2 0.071 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 75.06 -153.03 REMARK 500 GLN A 77 54.61 -96.52 REMARK 500 VAL A 124 -74.41 -95.00 REMARK 500 THR A 201 -43.51 -132.66 REMARK 500 PHE A 206 -51.07 -123.05 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. 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 86.2 REMARK 620 3 RIS A 400 O17 94.6 81.4 REMARK 620 4 DOD A 501 O 92.3 176.1 95.1 REMARK 620 5 DOD A 502 O 88.3 98.6 177.1 85.1 REMARK 620 6 DOD A 503 O 174.4 93.4 90.9 88.4 86.2 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 87.6 REMARK 620 3 RIS A 400 O12 96.0 172.9 REMARK 620 4 RIS A 400 O17 93.4 81.1 92.6 REMARK 620 5 DOD A 504 O 168.5 85.5 91.9 94.6 REMARK 620 6 DOD A 505 O 81.3 96.7 89.9 174.4 90.3 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 400 O10 94.5 REMARK 620 3 RIS A 400 O15 97.4 91.7 REMARK 620 4 DOD A 506 O 86.0 179.2 88.9 REMARK 620 5 DOD A 507 O 85.8 85.6 175.9 93.9 REMARK 620 6 DOD A 508 O 168.8 93.5 90.1 85.9 87.0 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 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CG6 RELATED DB: PDB DBREF 5CG5 A 8 353 UNP P14324 FPPS_HUMAN 74 419 SEQADV 5CG5 MET A 7 UNP P14324 INITIATING METHIONINE SEQADV 5CG5 LEU A 354 UNP P14324 EXPRESSION TAG SEQADV 5CG5 GLU A 355 UNP P14324 EXPRESSION TAG SEQADV 5CG5 HIS A 356 UNP P14324 EXPRESSION TAG SEQADV 5CG5 HIS A 357 UNP P14324 EXPRESSION TAG SEQADV 5CG5 HIS A 358 UNP P14324 EXPRESSION TAG SEQADV 5CG5 HIS A 359 UNP P14324 EXPRESSION TAG SEQADV 5CG5 HIS A 360 UNP P14324 EXPRESSION TAG SEQADV 5CG5 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 400 24 HETNAM MG MAGNESIUM ION HETNAM RIS 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID HETSYN RIS RISEDRONATE FORMUL 2 MG 3(MG 2+) FORMUL 5 RIS C7 H11 N O7 P2 FORMUL 6 DOD *106(D2 O) HELIX 1 AA1 ASP A 8 GLU A 30 1 23 HELIX 2 AA2 HIS A 35 GLU A 37 5 3 HELIX 3 AA3 ILE A 38 ALA A 53 1 16 HELIX 4 AA4 TYR A 58 VAL A 72 1 15 HELIX 5 AA5 GLU A 73 GLN A 77 5 5 HELIX 6 AA6 ASP A 78 ASP A 107 1 30 HELIX 7 AA7 TRP A 118 LYS A 121 5 4 HELIX 8 AA8 VAL A 124 LEU A 126 5 3 HELIX 9 AA9 ASP A 127 ARG A 148 1 22 HELIX 10 AB1 TYR A 152 ALA A 178 1 27 HELIX 11 AB2 ASP A 184 PHE A 188 5 5 HELIX 12 AB3 THR A 189 THR A 201 1 13 HELIX 13 AB4 THR A 201 PHE A 206 1 6 HELIX 14 AB5 PHE A 206 ALA A 217 1 12 HELIX 15 AB6 GLY A 221 GLY A 250 1 30 HELIX 16 AB7 ASP A 251 GLY A 256 1 6 HELIX 17 AB8 SER A 268 ALA A 278 1 11 HELIX 18 AB9 THR A 279 TYR A 290 1 12 HELIX 19 AC1 GLU A 294 LEU A 308 1 15 HELIX 20 AC2 ASP A 309 ALA A 333 1 25 HELIX 21 AC3 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 2.12 LINK OD2 ASP A 103 MG MG A 402 1555 1555 2.09 LINK OD2 ASP A 107 MG MG A 401 1555 1555 2.13 LINK OD2 ASP A 107 MG MG A 402 1555 1555 2.22 LINK OD2 ASP A 243 MG MG A 403 1555 1555 2.19 LINK O17 RIS A 400 MG MG A 401 1555 1555 2.14 LINK O12 RIS A 400 MG MG A 402 1555 1555 2.03 LINK O17 RIS A 400 MG MG A 402 1555 1555 2.05 LINK O10 RIS A 400 MG MG A 403 1555 1555 1.95 LINK O15 RIS A 400 MG MG A 403 1555 1555 2.05 LINK MG MG A 401 O DOD A 501 1555 1555 2.09 LINK MG MG A 401 O DOD A 502 1555 1555 2.12 LINK MG MG A 401 O DOD A 503 1555 1555 2.03 LINK MG MG A 402 O DOD A 504 1555 1555 2.08 LINK MG MG A 402 O DOD A 505 1555 1555 2.11 LINK MG MG A 403 O DOD A 506 1555 1555 2.03 LINK MG MG A 403 O DOD A 507 1555 1555 2.18 LINK MG MG A 403 O DOD A 508 1555 1555 2.17 CISPEP 1 ALA A 334 PRO A 335 0 8.29 SITE 1 AC1 7 ASP A 103 ASP A 107 RIS A 400 MG A 402 SITE 2 AC1 7 DOD A 501 DOD A 502 DOD A 503 SITE 1 AC2 6 ASP A 103 ASP A 107 RIS A 400 MG A 401 SITE 2 AC2 6 DOD A 504 DOD A 505 SITE 1 AC3 5 ASP A 243 RIS A 400 DOD A 506 DOD A 507 SITE 2 AC3 5 DOD A 508 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 ASP A 243 LYS A 257 SITE 3 AC4 22 MG A 401 MG A 402 MG A 403 DOD A 501 SITE 4 AC4 22 DOD A 503 DOD A 504 DOD A 505 DOD A 506 SITE 5 AC4 22 DOD A 507 DOD A 508 DOD A 509 DOD A 510 SITE 6 AC4 22 DOD A 523 DOD A 529 CRYST1 111.966 111.966 72.754 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 0.008931 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008931 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013745 0.00000