PDB Short entry for 2E94 HEADER TRANSFERASE 24-JAN-07 2E94 TITLE S. CEREVISIAE GERANYLGERANYL PYROPHOSPHATE SYNTHASE IN TITLE 2 COMPLEX WITH MAGNESIUM AND BPH-364 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GERANYLGERANYL PYROPHOSPHATE SYNTHETASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GGPP SYNTHETASE, GGPPSASE, GERANYLGERANYL COMPND 5 DIPHOSPHATE SYNTHASE, BET2 SUPPRESSOR PROTEIN 1; COMPND 6 EC: 2.5.1.30; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET32/LIC KEYWDS PRENYLTRANSFERASE, FARNESYL PYROPHOSPHATE, BISPHOSPHONATE EXPDTA X-RAY DIFFRACTION AUTHOR R.T.GUO,T.P.KO,R.CAO,C.K.-M.CHEN,W.Y.JENG,T.H.CHANG, AUTHOR 2 P.H.LIANG,E.OLDFIELD,A.H.-J.WANG REVDAT 3 24-FEB-09 2E94 1 VERSN REVDAT 2 19-JUN-07 2E94 1 JRNL REVDAT 1 12-JUN-07 2E94 0 JRNL AUTH R.T.GUO,R.CAO,P.H.LIANG,T.P.KO,T.H.CHANG, JRNL AUTH 2 M.P.HUDOCK,W.Y.JENG,C.K.-M.CHEN,Y.ZHANG,Y.SONG, JRNL AUTH 3 C.J.KUO,F.YIN,E.OLDFIELD,A.H.-J.WANG JRNL TITL BISPHOSPHONATES TARGET MULTIPLE SITES IN BOTH CIS- JRNL TITL 2 AND TRANS-PRENYLTRANSFERASES JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 10022 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17535895 JRNL DOI 10.1073/PNAS.0702254104 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 35219 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 SET) : 0.180 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1744 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.18 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2100 REMARK 3 BIN FREE R VALUE : 0.2550 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 123 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4954 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 657 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.20 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2E94 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JAN-07. REMARK 100 THE RCSB ID CODE IS RCSB026380. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36250 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 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 (%) : 96.8 REMARK 200 DATA REDUNDANCY : 5.360 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.16800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2DH4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08M CH3COONA, 16% PEG 4000, 6-10% REMARK 280 GLYCEROL, 6-10% 1,2-PROPANEDIOL, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 23.28500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.27250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.19650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.27250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.28500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.19650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 8720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 1 REMARK 465 HIS A 194 REMARK 465 HIS A 195 REMARK 465 ASP A 307 REMARK 465 ASN A 308 REMARK 465 GLU A 309 REMARK 465 ASN A 310 REMARK 465 LYS A 311 REMARK 465 TYR A 312 REMARK 465 LEU A 313 REMARK 465 PRO A 314 REMARK 465 ASP A 315 REMARK 465 LEU A 316 REMARK 465 ALA A 317 REMARK 465 SER A 318 REMARK 465 HIS A 319 REMARK 465 SER A 320 REMARK 465 ASP A 321 REMARK 465 THR A 322 REMARK 465 ALA A 323 REMARK 465 THR A 324 REMARK 465 ASN A 325 REMARK 465 LEU A 326 REMARK 465 HIS A 327 REMARK 465 ASP A 328 REMARK 465 GLU A 329 REMARK 465 LEU A 330 REMARK 465 LEU A 331 REMARK 465 TYR A 332 REMARK 465 ILE A 333 REMARK 465 ILE A 334 REMARK 465 ASP A 335 REMARK 465 HIS A 336 REMARK 465 LEU A 337 REMARK 465 SER A 338 REMARK 465 GLU A 339 REMARK 465 LEU A 340 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 SER B 193 REMARK 465 HIS B 194 REMARK 465 HIS B 195 REMARK 465 GLY B 196 REMARK 465 GLU B 227 REMARK 465 LYS B 228 REMARK 465 ASP B 315 REMARK 465 LEU B 316 REMARK 465 ALA B 317 REMARK 465 SER B 318 REMARK 465 HIS B 319 REMARK 465 SER B 320 REMARK 465 ASP B 321 REMARK 465 THR B 322 REMARK 465 ALA B 323 REMARK 465 THR B 324 REMARK 465 ASN B 325 REMARK 465 LEU B 326 REMARK 465 HIS B 327 REMARK 465 ASP B 328 REMARK 465 GLU B 329 REMARK 465 LEU B 330 REMARK 465 LEU B 331 REMARK 465 TYR B 332 REMARK 465 ILE B 333 REMARK 465 ILE B 334 REMARK 465 ASP B 335 REMARK 465 HIS B 336 REMARK 465 LEU B 337 REMARK 465 SER B 338 REMARK 465 GLU B 339 REMARK 465 LEU B 340 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 N GLY A 196 O HOH A 956 2.09 REMARK 500 OAD 364 A 1101 O HOH A 401 2.09 REMARK 500 OAB 364 A 1101 O HOH A 401 2.17 REMARK 500 OAD 364 B 1102 O HOH B 1057 2.19 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 LEU B 140 CA - CB - CG ANGL. DEV. = -16.8 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 PRO A 39 -161.41 -78.41 REMARK 500 ARG A 53 4.40 -64.14 REMARK 500 SER A 192 -112.14 -41.63 REMARK 500 LEU B 37 18.63 -64.55 REMARK 500 LYS B 59 -42.62 -26.22 REMARK 500 PRO B 158 32.69 -92.79 REMARK 500 LYS B 174 -71.03 -61.85 REMARK 500 SER B 225 114.61 168.09 REMARK 500 ASN B 306 31.97 -90.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR B 210 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 624 DISTANCE = 5.15 ANGSTROMS REMARK 525 HOH A 579 DISTANCE = 5.77 ANGSTROMS REMARK 525 HOH B 694 DISTANCE = 5.65 ANGSTROMS REMARK 525 HOH A 623 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B 702 DISTANCE = 5.10 ANGSTROMS REMARK 525 HOH B 721 DISTANCE = 5.37 ANGSTROMS REMARK 525 HOH B 733 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH B 751 DISTANCE = 8.46 ANGSTROMS REMARK 525 HOH B 754 DISTANCE = 8.24 ANGSTROMS REMARK 525 HOH B 780 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH B 781 DISTANCE = 7.59 ANGSTROMS REMARK 525 HOH A 705 DISTANCE = 9.84 ANGSTROMS REMARK 525 HOH B 794 DISTANCE = 8.57 ANGSTROMS REMARK 525 HOH A 707 DISTANCE = 5.06 ANGSTROMS REMARK 525 HOH B 800 DISTANCE = 7.20 ANGSTROMS REMARK 525 HOH A 710 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH B 814 DISTANCE = 9.26 ANGSTROMS REMARK 525 HOH B 818 DISTANCE = 5.78 ANGSTROMS REMARK 525 HOH B 821 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B 825 DISTANCE = 5.17 ANGSTROMS REMARK 525 HOH B 830 DISTANCE = 9.91 ANGSTROMS REMARK 525 HOH B 834 DISTANCE = 8.95 ANGSTROMS REMARK 525 HOH B 835 DISTANCE = 9.62 ANGSTROMS REMARK 525 HOH B 837 DISTANCE = 10.87 ANGSTROMS REMARK 525 HOH A 745 DISTANCE = 7.58 ANGSTROMS REMARK 525 HOH A 746 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A 748 DISTANCE = 8.01 ANGSTROMS REMARK 525 HOH B 844 DISTANCE = 5.15 ANGSTROMS REMARK 525 HOH B 849 DISTANCE = 7.44 ANGSTROMS REMARK 525 HOH A 765 DISTANCE = 8.05 ANGSTROMS REMARK 525 HOH A 774 DISTANCE = 7.20 ANGSTROMS REMARK 525 HOH A 779 DISTANCE = 5.33 ANGSTROMS REMARK 525 HOH B 874 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH B 875 DISTANCE = 7.63 ANGSTROMS REMARK 525 HOH B 876 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH B 877 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH B 878 DISTANCE = 7.06 ANGSTROMS REMARK 525 HOH B 879 DISTANCE = 9.54 ANGSTROMS REMARK 525 HOH B 880 DISTANCE = 8.99 ANGSTROMS REMARK 525 HOH A 807 DISTANCE = 7.24 ANGSTROMS REMARK 525 HOH A 809 DISTANCE = 5.63 ANGSTROMS REMARK 525 HOH A 811 DISTANCE = 7.12 ANGSTROMS REMARK 525 HOH B 887 DISTANCE = 5.76 ANGSTROMS REMARK 525 HOH B 888 DISTANCE = 5.60 ANGSTROMS REMARK 525 HOH B 889 DISTANCE = 7.49 ANGSTROMS REMARK 525 HOH B 892 DISTANCE = 10.35 ANGSTROMS REMARK 525 HOH B 893 DISTANCE = 7.32 ANGSTROMS REMARK 525 HOH A 831 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A 832 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 833 DISTANCE = 8.80 ANGSTROMS REMARK 525 HOH B 897 DISTANCE = 6.96 ANGSTROMS REMARK 525 HOH A 890 DISTANCE = 10.61 ANGSTROMS REMARK 525 HOH B 905 DISTANCE = 5.56 ANGSTROMS REMARK 525 HOH A 927 DISTANCE = 7.71 ANGSTROMS REMARK 525 HOH B 912 DISTANCE = 8.48 ANGSTROMS REMARK 525 HOH B 913 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH B 951 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH B 981 DISTANCE = 8.74 ANGSTROMS REMARK 525 HOH B 982 DISTANCE = 8.46 ANGSTROMS REMARK 525 HOH B1006 DISTANCE = 8.14 ANGSTROMS REMARK 525 HOH B1008 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A 952 DISTANCE = 7.42 ANGSTROMS REMARK 525 HOH A 953 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH B1012 DISTANCE = 9.61 ANGSTROMS REMARK 525 HOH A 954 DISTANCE = 8.54 ANGSTROMS REMARK 525 HOH B1013 DISTANCE = 7.18 ANGSTROMS REMARK 525 HOH A 955 DISTANCE = 8.20 ANGSTROMS REMARK 525 HOH B1029 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH B1036 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH A 970 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH B1054 DISTANCE = 6.87 ANGSTROMS REMARK 525 HOH A 973 DISTANCE = 5.78 ANGSTROMS REMARK 525 HOH A 976 DISTANCE = 7.17 ANGSTROMS REMARK 525 HOH A 977 DISTANCE = 8.94 ANGSTROMS REMARK 525 HOH A 978 DISTANCE = 9.35 ANGSTROMS REMARK 525 HOH A 979 DISTANCE = 12.26 ANGSTROMS REMARK 525 HOH A 980 DISTANCE = 12.14 ANGSTROMS REMARK 525 HOH A 984 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 988 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A1023 DISTANCE = 5.21 ANGSTROMS REMARK 525 HOH A1045 DISTANCE = 5.58 ANGSTROMS REMARK 525 HOH A1046 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A1050 DISTANCE = 11.24 ANGSTROMS REMARK 525 HOH A1053 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A1056 DISTANCE = 7.34 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 84 OD2 REMARK 620 2 364 A1101 OAA 85.6 REMARK 620 3 HOH A 601 O 74.8 75.9 REMARK 620 4 ASP A 80 OD1 86.7 91.4 158.1 REMARK 620 5 ASP A 80 OD2 67.7 50.6 114.7 45.6 REMARK 620 6 HOH A 776 O 105.4 165.8 115.2 80.5 125.0 REMARK 620 7 364 A1101 OAF 161.7 77.9 93.4 101.4 106.4 92.2 REMARK 620 N 1 2 3 4 5 6 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 1201 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 364 A 1101 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 364 B 1102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DH4 RELATED DB: PDB REMARK 900 NATIVE PROTEIN WITHOUT LIGAND REMARK 900 RELATED ID: 2E8T RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM, FSPP AND IPP REMARK 900 RELATED ID: 2E8U RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND IPP (IN REMARK 900 SPACE GROUP, P21) REMARK 900 RELATED ID: 2E8V RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH PRODUCT GGPP (IN SPACE REMARK 900 GROUP, P21) REMARK 900 RELATED ID: 2E8W RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND IPP REMARK 900 RELATED ID: 2E8X RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND GPP REMARK 900 RELATED ID: 2E90 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM, PYROPHOSPHATE REMARK 900 AND FPP REMARK 900 RELATED ID: 2E91 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH-91 REMARK 900 RELATED ID: 2E92 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH- REMARK 900 261(MINODRONATE) REMARK 900 RELATED ID: 2E93 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH BPH-629 REMARK 900 RELATED ID: 2E95 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH-675 REMARK 900 RELATED ID: 2E96 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH BPH-715 REMARK 900 RELATED ID: 2E97 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM, IPP AND BPH-715 DBREF 2E94 A 6 340 UNP Q12051 GGPPS_YEAST 1 335 DBREF 2E94 B 6 340 UNP Q12051 GGPPS_YEAST 1 335 SEQADV 2E94 MET A 1 UNP Q12051 CLONING ARTIFACT SEQADV 2E94 THR A 2 UNP Q12051 CLONING ARTIFACT SEQADV 2E94 LYS A 3 UNP Q12051 CLONING ARTIFACT SEQADV 2E94 ASN A 4 UNP Q12051 CLONING ARTIFACT SEQADV 2E94 LYS A 5 UNP Q12051 CLONING ARTIFACT SEQADV 2E94 MET B 1 UNP Q12051 CLONING ARTIFACT SEQADV 2E94 THR B 2 UNP Q12051 CLONING ARTIFACT SEQADV 2E94 LYS B 3 UNP Q12051 CLONING ARTIFACT SEQADV 2E94 ASN B 4 UNP Q12051 CLONING ARTIFACT SEQADV 2E94 LYS B 5 UNP Q12051 CLONING ARTIFACT SEQRES 1 A 340 MET THR LYS ASN LYS MET GLU ALA LYS ILE ASP GLU LEU SEQRES 2 A 340 ILE ASN ASN ASP PRO VAL TRP SER SER GLN ASN GLU SER SEQRES 3 A 340 LEU ILE SER LYS PRO TYR ASN HIS ILE LEU LEU LYS PRO SEQRES 4 A 340 GLY LYS ASN PHE ARG LEU ASN LEU ILE VAL GLN ILE ASN SEQRES 5 A 340 ARG VAL MET ASN LEU PRO LYS ASP GLN LEU ALA ILE VAL SEQRES 6 A 340 SER GLN ILE VAL GLU LEU LEU HIS ASN SER SER LEU LEU SEQRES 7 A 340 ILE ASP ASP ILE GLU ASP ASN ALA PRO LEU ARG ARG GLY SEQRES 8 A 340 GLN THR THR SER HIS LEU ILE PHE GLY VAL PRO SER THR SEQRES 9 A 340 ILE ASN THR ALA ASN TYR MET TYR PHE ARG ALA MET GLN SEQRES 10 A 340 LEU VAL SER GLN LEU THR THR LYS GLU PRO LEU TYR HIS SEQRES 11 A 340 ASN LEU ILE THR ILE PHE ASN GLU GLU LEU ILE ASN LEU SEQRES 12 A 340 HIS ARG GLY GLN GLY LEU ASP ILE TYR TRP ARG ASP PHE SEQRES 13 A 340 LEU PRO GLU ILE ILE PRO THR GLN GLU MET TYR LEU ASN SEQRES 14 A 340 MET VAL MET ASN LYS THR GLY GLY LEU PHE ARG LEU THR SEQRES 15 A 340 LEU ARG LEU MET GLU ALA LEU SER PRO SER SER HIS HIS SEQRES 16 A 340 GLY HIS SER LEU VAL PRO PHE ILE ASN LEU LEU GLY ILE SEQRES 17 A 340 ILE TYR GLN ILE ARG ASP ASP TYR LEU ASN LEU LYS ASP SEQRES 18 A 340 PHE GLN MET SER SER GLU LYS GLY PHE ALA GLU ASP ILE SEQRES 19 A 340 THR GLU GLY LYS LEU SER PHE PRO ILE VAL HIS ALA LEU SEQRES 20 A 340 ASN PHE THR LYS THR LYS GLY GLN THR GLU GLN HIS ASN SEQRES 21 A 340 GLU ILE LEU ARG ILE LEU LEU LEU ARG THR SER ASP LYS SEQRES 22 A 340 ASP ILE LYS LEU LYS LEU ILE GLN ILE LEU GLU PHE ASP SEQRES 23 A 340 THR ASN SER LEU ALA TYR THR LYS ASN PHE ILE ASN GLN SEQRES 24 A 340 LEU VAL ASN MET ILE LYS ASN ASP ASN GLU ASN LYS TYR SEQRES 25 A 340 LEU PRO ASP LEU ALA SER HIS SER ASP THR ALA THR ASN SEQRES 26 A 340 LEU HIS ASP GLU LEU LEU TYR ILE ILE ASP HIS LEU SER SEQRES 27 A 340 GLU LEU SEQRES 1 B 340 MET THR LYS ASN LYS MET GLU ALA LYS ILE ASP GLU LEU SEQRES 2 B 340 ILE ASN ASN ASP PRO VAL TRP SER SER GLN ASN GLU SER SEQRES 3 B 340 LEU ILE SER LYS PRO TYR ASN HIS ILE LEU LEU LYS PRO SEQRES 4 B 340 GLY LYS ASN PHE ARG LEU ASN LEU ILE VAL GLN ILE ASN SEQRES 5 B 340 ARG VAL MET ASN LEU PRO LYS ASP GLN LEU ALA ILE VAL SEQRES 6 B 340 SER GLN ILE VAL GLU LEU LEU HIS ASN SER SER LEU LEU SEQRES 7 B 340 ILE ASP ASP ILE GLU ASP ASN ALA PRO LEU ARG ARG GLY SEQRES 8 B 340 GLN THR THR SER HIS LEU ILE PHE GLY VAL PRO SER THR SEQRES 9 B 340 ILE ASN THR ALA ASN TYR MET TYR PHE ARG ALA MET GLN SEQRES 10 B 340 LEU VAL SER GLN LEU THR THR LYS GLU PRO LEU TYR HIS SEQRES 11 B 340 ASN LEU ILE THR ILE PHE ASN GLU GLU LEU ILE ASN LEU SEQRES 12 B 340 HIS ARG GLY GLN GLY LEU ASP ILE TYR TRP ARG ASP PHE SEQRES 13 B 340 LEU PRO GLU ILE ILE PRO THR GLN GLU MET TYR LEU ASN SEQRES 14 B 340 MET VAL MET ASN LYS THR GLY GLY LEU PHE ARG LEU THR SEQRES 15 B 340 LEU ARG LEU MET GLU ALA LEU SER PRO SER SER HIS HIS SEQRES 16 B 340 GLY HIS SER LEU VAL PRO PHE ILE ASN LEU LEU GLY ILE SEQRES 17 B 340 ILE TYR GLN ILE ARG ASP ASP TYR LEU ASN LEU LYS ASP SEQRES 18 B 340 PHE GLN MET SER SER GLU LYS GLY PHE ALA GLU ASP ILE SEQRES 19 B 340 THR GLU GLY LYS LEU SER PHE PRO ILE VAL HIS ALA LEU SEQRES 20 B 340 ASN PHE THR LYS THR LYS GLY GLN THR GLU GLN HIS ASN SEQRES 21 B 340 GLU ILE LEU ARG ILE LEU LEU LEU ARG THR SER ASP LYS SEQRES 22 B 340 ASP ILE LYS LEU LYS LEU ILE GLN ILE LEU GLU PHE ASP SEQRES 23 B 340 THR ASN SER LEU ALA TYR THR LYS ASN PHE ILE ASN GLN SEQRES 24 B 340 LEU VAL ASN MET ILE LYS ASN ASP ASN GLU ASN LYS TYR SEQRES 25 B 340 LEU PRO ASP LEU ALA SER HIS SER ASP THR ALA THR ASN SEQRES 26 B 340 LEU HIS ASP GLU LEU LEU TYR ILE ILE ASP HIS LEU SER SEQRES 27 B 340 GLU LEU HET MG A1201 1 HET 364 A1101 29 HET 364 B1102 29 HETNAM MG MAGNESIUM ION HETNAM 364 3-BIPHENYL-3-YL-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL) HETNAM 2 364 PYRIDINIUM HETSYN 364 3-BIPHENYL-3-YL-1-(2-HYDROXY-2,2-BIS-PHOSPHONO-ETHYL)- HETSYN 2 364 PYRIDINIUM FORMUL 3 MG MG 2+ FORMUL 4 364 2(C19 H20 N O7 P2 1+) FORMUL 6 HOH *657(H2 O) HELIX 1 1 ASN A 4 ASN A 15 1 12 HELIX 2 2 SER A 21 LEU A 37 1 17 HELIX 3 3 GLY A 40 ASN A 56 1 17 HELIX 4 4 PRO A 58 ASN A 85 1 28 HELIX 5 5 THR A 94 GLY A 100 1 7 HELIX 6 6 GLY A 100 VAL A 119 1 20 HELIX 7 7 SER A 120 THR A 123 5 4 HELIX 8 8 LYS A 125 PHE A 156 1 32 HELIX 9 9 THR A 163 THR A 175 1 13 HELIX 10 10 THR A 175 SER A 190 1 16 HELIX 11 11 LEU A 199 SER A 225 1 27 HELIX 12 12 ALA A 231 GLY A 237 1 7 HELIX 13 13 SER A 240 LYS A 253 1 14 HELIX 14 14 GLN A 255 ARG A 269 1 15 HELIX 15 15 ASP A 272 ASP A 286 1 15 HELIX 16 16 ASN A 288 ASN A 306 1 19 HELIX 17 17 LYS B 3 ASN B 15 1 13 HELIX 18 18 SER B 21 LEU B 37 1 17 HELIX 19 19 GLY B 40 ASN B 56 1 17 HELIX 20 20 PRO B 58 ASP B 84 1 27 HELIX 21 21 THR B 94 GLY B 100 1 7 HELIX 22 22 GLY B 100 SER B 120 1 21 HELIX 23 23 LYS B 125 LEU B 157 1 33 HELIX 24 24 THR B 163 THR B 175 1 13 HELIX 25 25 THR B 175 SER B 190 1 16 HELIX 26 26 LEU B 199 MET B 224 1 26 HELIX 27 27 ALA B 231 GLY B 237 1 7 HELIX 28 28 SER B 240 LYS B 253 1 14 HELIX 29 29 GLN B 255 ARG B 269 1 15 HELIX 30 30 ASP B 272 ASP B 286 1 15 HELIX 31 31 ASN B 288 ASN B 306 1 19 SHEET 1 A 2 LEU A 88 ARG A 89 0 SHEET 2 A 2 GLN A 92 THR A 93 -1 O GLN A 92 N ARG A 89 SHEET 1 B 2 LEU B 88 ARG B 89 0 SHEET 2 B 2 GLN B 92 THR B 93 -1 O GLN B 92 N ARG B 89 LINK MG MG A1201 OD2 ASP A 84 1555 1555 2.35 LINK MG MG A1201 OAA 364 A1101 1555 1555 2.44 LINK MG MG A1201 O HOH A 601 1555 1555 2.58 LINK MG MG A1201 OD1 ASP A 80 1555 1555 2.66 LINK MG MG A1201 OD2 ASP A 80 1555 1555 2.98 LINK MG MG A1201 O HOH A 776 1555 1555 2.72 LINK MG MG A1201 OAF 364 A1101 1555 1555 2.47 CISPEP 1 LEU A 157 PRO A 158 0 0.66 CISPEP 2 LEU B 157 PRO B 158 0 0.37 SITE 1 AC1 5 ASP A 80 ASP A 84 HOH A 601 HOH A 776 SITE 2 AC1 5 364 A1101 SITE 1 AC2 18 VAL A 69 HIS A 73 ASP A 80 ASP A 84 SITE 2 AC2 18 ARG A 89 LYS A 174 LEU A 178 PHE A 179 SITE 3 AC2 18 THR A 182 TYR A 210 GLN A 211 ASP A 214 SITE 4 AC2 18 LYS A 238 HOH A 401 HOH A 601 HOH A 708 SITE 5 AC2 18 HOH A 983 MG A1201 SITE 1 AC3 13 HIS B 73 ASP B 80 ASP B 84 ARG B 89 SITE 2 AC3 13 LYS B 174 LEU B 178 THR B 182 TYR B 210 SITE 3 AC3 13 GLN B 211 ASP B 214 LYS B 238 HOH B 548 SITE 4 AC3 13 HOH B1057 CRYST1 46.570 116.393 128.545 90.00 90.00 90.00 P 21 21 21 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 0.021473 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008592 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007779 0.00000