HEADER TRANSFERASE/TRANSFERASE INHIBITOR 26-JUN-07 2Z4Y TITLE S. CEREVISIAE GERANYLGERANYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH TITLE 2 MAGNESIUM AND BPH-252 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GERANYLGERANYL PYROPHOSPHATE SYNTHETASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GGPP SYNTHETASE, GGPPSASE, GERANYLGERANYL DIPHOSPHATE COMPND 5 SYNTHASE, BET2 SUPPRESSOR PROTEIN 1; COMPND 6 EC: 2.5.1.30, 2.5.1.1, 2.5.1.10, 2.5.1.29; 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 XA/LIC KEYWDS PRENYLTRANSFERASE, GERANYLGERANYL PYROPHOSPHATE, BISPHOSPHONATE, KEYWDS 2 TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.K.-M.CHEN,R.T.GUO,M.HUDOCK,R.CAO,E.OLDFIELD,A.H.-J.WANG REVDAT 3 29-DEC-10 2Z4Y 1 JRNL HEADER KEYWDS REVDAT 2 24-FEB-09 2Z4Y 1 VERSN REVDAT 1 01-JUL-08 2Z4Y 0 JRNL AUTH C.K.-M.CHEN,M.P.HUDOCK,Y.ZHANG,R.-T.GUO,R.CAO,J.H.NO, JRNL AUTH 2 P.-H.LIANG,T.-P.KO,T.-H.CHANG,S.-C.CHANG,Y.SONG,J.AXELSON, JRNL AUTH 3 A.KUMAR,A.H.-J.WANG,E.OLDFIELD JRNL TITL INHIBITION OF GERANYLGERANYL DIPHOSPHATE SYNTHASE BY JRNL TITL 2 BISPHOSPHONATES: A CRYSTALLOGRAPHIC AND COMPUTATIONAL JRNL TITL 3 INVESTIGATION JRNL REF J.MED.CHEM. V. 51 5594 2008 JRNL REFN ISSN 0022-2623 JRNL PMID 18800762 JRNL DOI 10.1021/JM800325Y REMARK 2 REMARK 2 RESOLUTION. 2.10 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 38785 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) : 0.181 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1942 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1970 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 199 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 : 4663 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 391 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.27 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 1.70 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 2Z4Y COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUN-07. REMARK 100 THE RCSB ID CODE IS RCSB027526. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-07 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 : SPRING-8 REMARK 200 BEAMLINE : BL12B2 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 : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40023 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.45300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 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 (%): 42.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 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, HANGING REMARK 280 DROP, TEMPERATURE 298K 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 22.97600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.01000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.10400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.01000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.97600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.10400 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: 8670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 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 THR A 2 REMARK 465 LYS A 3 REMARK 465 LYS A 41 REMARK 465 ASN A 42 REMARK 465 PHE A 43 REMARK 465 SER A 192 REMARK 465 SER A 193 REMARK 465 HIS A 194 REMARK 465 HIS A 195 REMARK 465 GLY A 196 REMARK 465 HIS A 197 REMARK 465 MET A 224 REMARK 465 SER A 225 REMARK 465 SER A 226 REMARK 465 GLU A 227 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 LYS B 3 REMARK 465 LYS B 38 REMARK 465 PRO B 39 REMARK 465 GLY B 40 REMARK 465 LYS B 41 REMARK 465 ASN B 42 REMARK 465 PHE B 43 REMARK 465 ARG B 44 REMARK 465 LEU B 45 REMARK 465 ASN B 46 REMARK 465 LEU B 47 REMARK 465 SER B 193 REMARK 465 HIS B 194 REMARK 465 HIS B 195 REMARK 465 GLY B 196 REMARK 465 HIS B 197 REMARK 465 GLN B 223 REMARK 465 MET B 224 REMARK 465 SER B 225 REMARK 465 SER B 226 REMARK 465 GLU B 227 REMARK 465 LYS B 228 REMARK 465 ASP B 307 REMARK 465 ASN B 308 REMARK 465 GLU B 309 REMARK 465 ASN B 310 REMARK 465 LYS B 311 REMARK 465 TYR B 312 REMARK 465 LEU B 313 REMARK 465 PRO B 314 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: 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 MET A 166 SD MET A 166 CE -0.339 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 THR A 94 N - CA - CB ANGL. DEV. = -11.7 DEGREES REMARK 500 LEU A 140 CA - CB - CG ANGL. DEV. = -14.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 46 -79.37 -60.10 REMARK 500 PRO A 158 30.71 -94.35 REMARK 500 LYS A 174 -70.12 -70.33 REMARK 500 ILE A 304 -87.76 -79.39 REMARK 500 LYS A 305 -43.16 -26.39 REMARK 500 LYS B 59 -14.98 -36.12 REMARK 500 PRO B 158 36.75 -95.30 REMARK 500 LYS B 174 -80.36 -65.90 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 A 110 0.07 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 B1340 DISTANCE = 8.11 ANGSTROMS REMARK 525 HOH A1255 DISTANCE = 5.75 ANGSTROMS REMARK 525 HOH B1365 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH B1379 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH A1292 DISTANCE = 5.06 ANGSTROMS REMARK 525 HOH B1392 DISTANCE = 5.72 ANGSTROMS REMARK 525 HOH A1309 DISTANCE = 7.28 ANGSTROMS REMARK 525 HOH A1314 DISTANCE = 6.87 ANGSTROMS REMARK 525 HOH B1415 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH B1416 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH B1422 DISTANCE = 9.33 ANGSTROMS REMARK 525 HOH B1423 DISTANCE = 8.55 ANGSTROMS REMARK 525 HOH A1329 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A1338 DISTANCE = 7.80 ANGSTROMS REMARK 525 HOH A1344 DISTANCE = 5.14 ANGSTROMS REMARK 525 HOH A1347 DISTANCE = 7.33 ANGSTROMS REMARK 525 HOH B1446 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH B1447 DISTANCE = 9.18 ANGSTROMS REMARK 525 HOH B1448 DISTANCE = 6.91 ANGSTROMS REMARK 525 HOH B1449 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH A1359 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A1360 DISTANCE = 8.24 ANGSTROMS REMARK 525 HOH B1469 DISTANCE = 7.32 ANGSTROMS REMARK 525 HOH A1377 DISTANCE = 5.19 ANGSTROMS REMARK 525 HOH A1385 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH A1387 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A1392 DISTANCE = 8.63 ANGSTROMS REMARK 525 HOH A1397 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH A1398 DISTANCE = 11.33 ANGSTROMS REMARK 525 HOH A1399 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH A1403 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A1416 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A1418 DISTANCE = 5.61 ANGSTROMS REMARK 525 HOH A1423 DISTANCE = 7.53 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 252 A 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 252 A 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 252 B 1203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Z4V RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND GGPP REMARK 900 (INHIBITORY SITE) REMARK 900 RELATED ID: 2Z4W RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH-749 REMARK 900 RELATED ID: 2Z4X RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH-252 (P21) REMARK 900 RELATED ID: 2Z4Z RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH-SC01 REMARK 900 RELATED ID: 2Z50 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH BPH-28 REMARK 900 RELATED ID: 2Z52 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH-23 DBREF 2Z4Y A 6 340 UNP Q12051 GGPPS_YEAST 1 335 DBREF 2Z4Y B 6 340 UNP Q12051 GGPPS_YEAST 1 335 SEQADV 2Z4Y MET A 1 UNP Q12051 EXPRESSION TAG SEQADV 2Z4Y THR A 2 UNP Q12051 EXPRESSION TAG SEQADV 2Z4Y LYS A 3 UNP Q12051 EXPRESSION TAG SEQADV 2Z4Y ASN A 4 UNP Q12051 EXPRESSION TAG SEQADV 2Z4Y LYS A 5 UNP Q12051 EXPRESSION TAG SEQADV 2Z4Y MET B 1 UNP Q12051 EXPRESSION TAG SEQADV 2Z4Y THR B 2 UNP Q12051 EXPRESSION TAG SEQADV 2Z4Y LYS B 3 UNP Q12051 EXPRESSION TAG SEQADV 2Z4Y ASN B 4 UNP Q12051 EXPRESSION TAG SEQADV 2Z4Y LYS B 5 UNP Q12051 EXPRESSION TAG 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 B1301 1 HET 252 A1201 18 HET 252 A1202 18 HET 252 B1203 18 HETNAM MG MAGNESIUM ION HETNAM 252 (1-HYDROXYNONANE-1,1-DIYL)BIS(PHOSPHONIC ACID) FORMUL 3 MG MG 2+ FORMUL 4 252 3(C9 H22 O7 P2) FORMUL 7 HOH *391(H2 O) HELIX 1 1 LYS A 5 ASN A 15 1 11 HELIX 2 2 SER A 21 LEU A 37 1 17 HELIX 3 3 ARG A 44 ASN A 56 1 13 HELIX 4 4 PRO A 58 ASP A 84 1 27 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 LEU A 122 5 3 HELIX 8 8 LYS A 125 PHE A 156 1 32 HELIX 9 9 THR A 163 SER A 190 1 28 HELIX 10 10 LEU A 199 ASP A 221 1 23 HELIX 11 11 ALA A 231 GLU A 236 1 6 HELIX 12 12 SER A 240 GLY A 254 1 15 HELIX 13 13 GLN A 255 ARG A 269 1 15 HELIX 14 14 ASP A 272 ASP A 286 1 15 HELIX 15 15 ASN A 288 ASN A 306 1 19 HELIX 16 16 ASN B 4 ASN B 15 1 12 HELIX 17 17 SER B 21 LEU B 37 1 17 HELIX 18 18 ILE B 51 ASN B 56 1 6 HELIX 19 19 PRO B 58 ASP B 84 1 27 HELIX 20 20 THR B 94 GLY B 100 1 7 HELIX 21 21 GLY B 100 SER B 120 1 21 HELIX 22 22 LYS B 125 LEU B 157 1 33 HELIX 23 23 THR B 163 SER B 190 1 28 HELIX 24 24 LEU B 199 ASP B 221 1 23 HELIX 25 25 ALA B 231 GLY B 237 1 7 HELIX 26 26 SER B 240 LYS B 253 1 14 HELIX 27 27 GLN B 255 LEU B 268 1 14 HELIX 28 28 ASP B 272 ASP B 286 1 15 HELIX 29 29 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 CISPEP 1 LEU A 157 PRO A 158 0 0.54 CISPEP 2 LEU B 157 PRO B 158 0 0.17 SITE 1 AC1 5 ASP B 214 LYS B 238 HOH B1356 HOH B1411 SITE 2 AC1 5 HOH B1438 SITE 1 AC2 9 ASP A 80 ARG A 89 LYS A 174 GLN A 211 SITE 2 AC2 9 ASP A 214 LYS A 238 HOH A1373 HOH A1375 SITE 3 AC2 9 HOH A1395 SITE 1 AC3 9 GLY A 40 ARG A 44 LEU A 47 HIS A 73 SITE 2 AC3 9 LEU A 77 ARG A 89 ARG A 90 TYR A 210 SITE 3 AC3 9 HOH A1373 SITE 1 AC4 13 ASP B 80 ARG B 89 LEU B 143 HIS B 144 SITE 2 AC4 13 LYS B 174 GLN B 211 ASP B 214 LYS B 238 SITE 3 AC4 13 HOH B1356 HOH B1411 HOH B1438 HOH B1439 SITE 4 AC4 13 HOH B1465 CRYST1 45.952 116.208 126.020 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 0.021762 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008605 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007935 0.00000