HEADER TRANSFERASE 27-JUL-08 3DYF TITLE T. BRUCEI FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH BISPHOSPHONATE TITLE 2 BPH-461 AND ISOPENTYL DIPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FARNESYL PYROPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.5.1.10; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-BISPHOSPHONATE COMPLEX, ISOPRENE BIOSYNTHESIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.CAO,Y.GAO,H.ROBINSON,A.GODDARD,E.OLDFIELD REVDAT 2 21-FEB-24 3DYF 1 REMARK SEQADV LINK REVDAT 1 05-MAY-09 3DYF 0 JRNL AUTH Y.ZHANG,R.CAO,F.YIN,M.P.HUDOCK,R.T.GUO,K.KRYSIAK, JRNL AUTH 2 S.MUKHERJEE,Y.G.GAO,H.ROBINSON,Y.SONG,J.H.NO,K.BERGAN, JRNL AUTH 3 A.LEON,L.CASS,A.GODDARD,T.K.CHANG,F.Y.LIN,E.VAN BEEK, JRNL AUTH 4 S.PAPAPOULOS,A.H.WANG,T.KUBO,M.OCHI,D.MUKKAMALA,E.OLDFIELD JRNL TITL LIPOPHILIC BISPHOSPHONATES AS DUAL FARNESYL/GERANYLGERANYL JRNL TITL 2 DIPHOSPHATE SYNTHASE INHIBITORS: AN X-RAY AND NMR JRNL TITL 3 INVESTIGATION. JRNL REF J.AM.CHEM.SOC. V. 131 5153 2009 JRNL REFN ISSN 0002-7863 JRNL PMID 19309137 JRNL DOI 10.1021/JA808285E REMARK 2 REMARK 2 RESOLUTION. 2.65 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) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 35680.210 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 25447 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) : 0.201 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1244 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.74 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2221 REMARK 3 BIN R VALUE (WORKING SET) : 0.2820 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 137 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5733 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 298 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.59000 REMARK 3 B22 (A**2) : -9.05000 REMARK 3 B33 (A**2) : 3.45000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 6.31000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.33 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 4.500 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.330 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.570 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.410 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 54.43 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 3DYF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048645. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 123.2 REMARK 200 PH : 5.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26721 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.13800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.58900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% MPD, 0.1 AMMONIUM ACETATE, PH REMARK 280 5.75, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 66.96950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.94900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 66.96950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 58.94900 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: 9950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 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 -22 REMARK 465 GLY A -21 REMARK 465 SER A -20 REMARK 465 SER A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 SER A -12 REMARK 465 SER A -11 REMARK 465 GLY A -10 REMARK 465 LEU A -9 REMARK 465 VAL A -8 REMARK 465 PRO A -7 REMARK 465 ARG A -6 REMARK 465 GLY A -5 REMARK 465 SER A -4 REMARK 465 HIS A -3 REMARK 465 MET A -2 REMARK 465 ALA A -1 REMARK 465 SER A 0 REMARK 465 LEU A 64 REMARK 465 SER A 65 REMARK 465 PRO A 66 REMARK 465 ASN A 67 REMARK 465 ASN A 68 REMARK 465 ASN A 69 REMARK 465 GLY A 70 REMARK 465 GLU A 71 REMARK 465 GLU A 72 REMARK 465 ASP A 73 REMARK 465 MET B -22 REMARK 465 GLY B -21 REMARK 465 SER B -20 REMARK 465 SER B -19 REMARK 465 HIS B -18 REMARK 465 HIS B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 SER B -12 REMARK 465 SER B -11 REMARK 465 GLY B -10 REMARK 465 LEU B -9 REMARK 465 VAL B -8 REMARK 465 PRO B -7 REMARK 465 ARG B -6 REMARK 465 GLY B -5 REMARK 465 SER B -4 REMARK 465 HIS B -3 REMARK 465 MET B -2 REMARK 465 ALA B -1 REMARK 465 SER B 0 REMARK 465 SER B 65 REMARK 465 PRO B 66 REMARK 465 ASN B 67 REMARK 465 ASN B 68 REMARK 465 ASN B 69 REMARK 465 GLY B 70 REMARK 465 GLU B 71 REMARK 465 GLU B 72 REMARK 465 ASP B 73 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 ASP A 26 67.18 32.01 REMARK 500 TYR A 48 19.52 58.07 REMARK 500 LEU A 61 22.05 -79.82 REMARK 500 TYR A 119 1.09 -64.06 REMARK 500 ASP A 181 105.74 -53.97 REMARK 500 LEU A 185 93.38 -46.67 REMARK 500 PHE A 197 16.60 58.78 REMARK 500 ALA A 198 -8.21 -51.12 REMARK 500 THR A 213 -49.65 -130.07 REMARK 500 TYR A 218 -51.98 -120.89 REMARK 500 PRO A 233 0.36 -66.57 REMARK 500 THR A 272 -4.18 -141.82 REMARK 500 LEU B 62 92.37 -51.02 REMARK 500 SER B 63 62.36 134.15 REMARK 500 ASP B 181 94.89 -61.84 REMARK 500 LEU B 185 107.44 -53.28 REMARK 500 ASP B 186 103.10 -165.72 REMARK 500 THR B 213 -60.87 -132.07 REMARK 500 GLU B 335 -72.30 -65.87 REMARK 500 THR B 362 -60.31 -97.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A3002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 OD2 REMARK 620 2 ASP A 107 OD2 78.0 REMARK 620 3 NI9 A3001 O7 73.3 69.1 REMARK 620 4 NI9 A3001 O3 114.2 136.3 74.7 REMARK 620 5 HOH A5225 O 148.4 79.8 78.0 69.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A3004 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 OD1 REMARK 620 2 NI9 A3001 O7 83.0 REMARK 620 3 HOH A5002 O 75.6 137.1 REMARK 620 4 HOH A5003 O 120.6 76.7 82.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A3003 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 255 OD2 REMARK 620 2 HOH A5001 O 158.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B4002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 103 OD1 REMARK 620 2 ASP B 107 OD2 76.4 REMARK 620 3 NI9 B4001 O3 129.5 137.5 REMARK 620 4 NI9 B4001 O7 87.0 65.9 81.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B4004 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 103 OD2 REMARK 620 2 ASP B 107 OD2 64.5 REMARK 620 3 NI9 B4001 O7 70.6 63.3 REMARK 620 4 HOH B5004 O 72.1 132.6 85.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B4003 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 255 OD2 REMARK 620 2 NI9 B4001 O6 91.7 REMARK 620 3 HOH B5161 O 156.2 84.1 REMARK 620 4 HOH B5264 O 71.9 94.7 85.1 REMARK 620 N 1 2 3 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 3002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 3003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 3004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 4002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 4003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 4004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI9 A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI9 B 4001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME B 9001 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPR B 6002 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPR A 6001 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 7001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2I19 RELATED DB: PDB REMARK 900 RELATED ID: 2EWG RELATED DB: PDB REMARK 900 RELATED ID: 2OGD RELATED DB: PDB REMARK 900 RELATED ID: 3DYG RELATED DB: PDB REMARK 900 RELATED ID: 3DYH RELATED DB: PDB DBREF 3DYF A 1 367 UNP Q86C09 Q86C09_9TRYP 1 367 DBREF 3DYF B 1 367 UNP Q86C09 Q86C09_9TRYP 1 367 SEQADV 3DYF MET A -22 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF GLY A -21 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF SER A -20 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF SER A -19 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF HIS A -18 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF HIS A -17 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF HIS A -16 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF HIS A -15 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF HIS A -14 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF HIS A -13 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF SER A -12 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF SER A -11 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF GLY A -10 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF LEU A -9 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF VAL A -8 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF PRO A -7 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF ARG A -6 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF GLY A -5 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF SER A -4 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF HIS A -3 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF MET A -2 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF ALA A -1 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF SER A 0 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF MET B -22 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF GLY B -21 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF SER B -20 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF SER B -19 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF HIS B -18 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF HIS B -17 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF HIS B -16 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF HIS B -15 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF HIS B -14 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF HIS B -13 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF SER B -12 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF SER B -11 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF GLY B -10 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF LEU B -9 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF VAL B -8 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF PRO B -7 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF ARG B -6 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF GLY B -5 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF SER B -4 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF HIS B -3 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF MET B -2 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF ALA B -1 UNP Q86C09 EXPRESSION TAG SEQADV 3DYF SER B 0 UNP Q86C09 EXPRESSION TAG SEQRES 1 A 390 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 390 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET PRO MET SEQRES 3 A 390 GLN MET PHE MET GLN VAL TYR ASP GLU ILE GLN MET PHE SEQRES 4 A 390 LEU LEU GLU GLU LEU GLU LEU LYS PHE ASP MET ASP PRO SEQRES 5 A 390 ASN ARG VAL ARG TYR LEU ARG LYS MET MET ASP THR THR SEQRES 6 A 390 CYS LEU GLY GLY LYS TYR ASN ARG GLY LEU THR VAL ILE SEQRES 7 A 390 ASP VAL ALA GLU SER LEU LEU SER LEU SER PRO ASN ASN SEQRES 8 A 390 ASN GLY GLU GLU ASP ASP GLY ALA ARG ARG LYS ARG VAL SEQRES 9 A 390 LEU HIS ASP ALA CYS VAL CYS GLY TRP MET ILE GLU PHE SEQRES 10 A 390 LEU GLN ALA HIS TYR LEU VAL GLU ASP ASP ILE MET ASP SEQRES 11 A 390 ASN SER VAL THR ARG ARG GLY LYS PRO CYS TRP TYR ARG SEQRES 12 A 390 HIS PRO ASP VAL THR VAL GLN CYS ALA ILE ASN ASP GLY SEQRES 13 A 390 LEU LEU LEU LYS SER TRP THR HIS MET MET ALA MET HIS SEQRES 14 A 390 PHE PHE ALA ASP ARG PRO PHE LEU GLN ASP LEU LEU CYS SEQRES 15 A 390 ARG PHE ASN ARG VAL ASP TYR THR THR ALA VAL GLY GLN SEQRES 16 A 390 LEU TYR ASP VAL THR SER MET PHE ASP SER ASN LYS LEU SEQRES 17 A 390 ASP PRO ASP VAL SER GLN PRO THR THR THR ASP PHE ALA SEQRES 18 A 390 GLU PHE THR LEU SER ASN TYR LYS ARG ILE VAL LYS TYR SEQRES 19 A 390 LYS THR ALA TYR TYR THR TYR LEU LEU PRO LEU VAL MET SEQRES 20 A 390 GLY LEU ILE VAL SER GLU ALA LEU PRO THR VAL ASP MET SEQRES 21 A 390 GLY VAL THR GLU GLU LEU ALA MET LEU MET GLY GLU TYR SEQRES 22 A 390 PHE GLN VAL GLN ASP ASP VAL MET ASP CYS PHE THR PRO SEQRES 23 A 390 PRO GLU ARG LEU GLY LYS VAL GLY THR ASP ILE GLN ASP SEQRES 24 A 390 ALA LYS CYS SER TRP LEU ALA VAL THR PHE LEU ALA LYS SEQRES 25 A 390 ALA SER SER ALA GLN VAL ALA GLU PHE LYS ALA ASN TYR SEQRES 26 A 390 GLY SER GLY ASP SER GLU LYS VAL ALA THR VAL ARG ARG SEQRES 27 A 390 LEU TYR GLU GLU ALA ASP LEU GLN GLY ASP TYR VAL ALA SEQRES 28 A 390 TYR GLU ALA ALA VAL ALA GLU GLN VAL LYS GLU LEU ILE SEQRES 29 A 390 GLU LYS LEU ARG LEU CYS SER PRO GLY PHE ALA ALA SER SEQRES 30 A 390 VAL GLU THR LEU TRP GLY LYS THR TYR LYS ARG GLN LYS SEQRES 1 B 390 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 390 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET PRO MET SEQRES 3 B 390 GLN MET PHE MET GLN VAL TYR ASP GLU ILE GLN MET PHE SEQRES 4 B 390 LEU LEU GLU GLU LEU GLU LEU LYS PHE ASP MET ASP PRO SEQRES 5 B 390 ASN ARG VAL ARG TYR LEU ARG LYS MET MET ASP THR THR SEQRES 6 B 390 CYS LEU GLY GLY LYS TYR ASN ARG GLY LEU THR VAL ILE SEQRES 7 B 390 ASP VAL ALA GLU SER LEU LEU SER LEU SER PRO ASN ASN SEQRES 8 B 390 ASN GLY GLU GLU ASP ASP GLY ALA ARG ARG LYS ARG VAL SEQRES 9 B 390 LEU HIS ASP ALA CYS VAL CYS GLY TRP MET ILE GLU PHE SEQRES 10 B 390 LEU GLN ALA HIS TYR LEU VAL GLU ASP ASP ILE MET ASP SEQRES 11 B 390 ASN SER VAL THR ARG ARG GLY LYS PRO CYS TRP TYR ARG SEQRES 12 B 390 HIS PRO ASP VAL THR VAL GLN CYS ALA ILE ASN ASP GLY SEQRES 13 B 390 LEU LEU LEU LYS SER TRP THR HIS MET MET ALA MET HIS SEQRES 14 B 390 PHE PHE ALA ASP ARG PRO PHE LEU GLN ASP LEU LEU CYS SEQRES 15 B 390 ARG PHE ASN ARG VAL ASP TYR THR THR ALA VAL GLY GLN SEQRES 16 B 390 LEU TYR ASP VAL THR SER MET PHE ASP SER ASN LYS LEU SEQRES 17 B 390 ASP PRO ASP VAL SER GLN PRO THR THR THR ASP PHE ALA SEQRES 18 B 390 GLU PHE THR LEU SER ASN TYR LYS ARG ILE VAL LYS TYR SEQRES 19 B 390 LYS THR ALA TYR TYR THR TYR LEU LEU PRO LEU VAL MET SEQRES 20 B 390 GLY LEU ILE VAL SER GLU ALA LEU PRO THR VAL ASP MET SEQRES 21 B 390 GLY VAL THR GLU GLU LEU ALA MET LEU MET GLY GLU TYR SEQRES 22 B 390 PHE GLN VAL GLN ASP ASP VAL MET ASP CYS PHE THR PRO SEQRES 23 B 390 PRO GLU ARG LEU GLY LYS VAL GLY THR ASP ILE GLN ASP SEQRES 24 B 390 ALA LYS CYS SER TRP LEU ALA VAL THR PHE LEU ALA LYS SEQRES 25 B 390 ALA SER SER ALA GLN VAL ALA GLU PHE LYS ALA ASN TYR SEQRES 26 B 390 GLY SER GLY ASP SER GLU LYS VAL ALA THR VAL ARG ARG SEQRES 27 B 390 LEU TYR GLU GLU ALA ASP LEU GLN GLY ASP TYR VAL ALA SEQRES 28 B 390 TYR GLU ALA ALA VAL ALA GLU GLN VAL LYS GLU LEU ILE SEQRES 29 B 390 GLU LYS LEU ARG LEU CYS SER PRO GLY PHE ALA ALA SER SEQRES 30 B 390 VAL GLU THR LEU TRP GLY LYS THR TYR LYS ARG GLN LYS HET MG A3002 1 HET MG A3003 1 HET MG A3004 1 HET ACT A8001 4 HET NI9 A3001 18 HET IPR A6001 14 HET MPD A7001 8 HET MG B4002 1 HET MG B4003 1 HET MG B4004 1 HET NI9 B4001 18 HET BME B9001 4 HET IPR B6002 14 HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM NI9 3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM HETNAM IPR ISOPENTYL PYROPHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM BME BETA-MERCAPTOETHANOL FORMUL 3 MG 6(MG 2+) FORMUL 6 ACT C2 H3 O2 1- FORMUL 7 NI9 2(C7 H11 F N O7 P2 1+) FORMUL 8 IPR 2(C5 H14 O7 P2) FORMUL 9 MPD C6 H14 O2 FORMUL 14 BME C2 H6 O S FORMUL 16 HOH *298(H2 O) HELIX 1 1 MET A 1 PHE A 25 1 25 HELIX 2 2 ASP A 28 LEU A 44 1 17 HELIX 3 3 TYR A 48 LEU A 61 1 14 HELIX 4 4 ASP A 74 ASN A 108 1 35 HELIX 5 5 CYS A 117 HIS A 121 5 5 HELIX 6 6 THR A 125 ALA A 149 1 25 HELIX 7 7 PHE A 153 VAL A 176 1 24 HELIX 8 8 THR A 201 THR A 213 1 13 HELIX 9 9 THR A 213 TYR A 218 1 6 HELIX 10 10 TYR A 218 SER A 229 1 12 HELIX 11 11 ALA A 231 VAL A 235 5 5 HELIX 12 12 ASP A 236 THR A 262 1 27 HELIX 13 13 PRO A 263 GLY A 268 1 6 HELIX 14 14 THR A 272 ALA A 277 1 6 HELIX 15 15 SER A 280 ALA A 290 1 11 HELIX 16 16 SER A 291 TYR A 302 1 12 HELIX 17 17 ASP A 306 GLU A 319 1 14 HELIX 18 18 ASP A 321 LEU A 346 1 26 HELIX 19 19 SER A 348 LYS A 361 1 14 HELIX 20 20 MET B 1 PHE B 25 1 25 HELIX 21 21 ASP B 28 LEU B 44 1 17 HELIX 22 22 TYR B 48 LEU B 62 1 15 HELIX 23 23 ASP B 74 ASP B 107 1 34 HELIX 24 24 TRP B 118 HIS B 121 5 4 HELIX 25 25 THR B 125 PHE B 148 1 24 HELIX 26 26 PHE B 153 THR B 177 1 25 HELIX 27 27 THR B 201 THR B 213 1 13 HELIX 28 28 THR B 213 TYR B 218 1 6 HELIX 29 29 TYR B 218 SER B 229 1 12 HELIX 30 30 ALA B 231 VAL B 235 5 5 HELIX 31 31 ASP B 236 THR B 262 1 27 HELIX 32 32 PRO B 263 GLY B 268 1 6 HELIX 33 33 SER B 280 ALA B 290 1 11 HELIX 34 34 SER B 291 ALA B 300 1 10 HELIX 35 35 ASP B 306 ALA B 320 1 15 HELIX 36 36 ASP B 321 SER B 348 1 28 HELIX 37 37 SER B 348 TYR B 363 1 16 SHEET 1 A 2 THR B 111 ARG B 112 0 SHEET 2 A 2 LYS B 115 PRO B 116 -1 O LYS B 115 N ARG B 112 LINK OD2 ASP A 103 MG MG A3002 1555 1555 2.22 LINK OD1 ASP A 103 MG MG A3004 1555 1555 2.42 LINK OD2 ASP A 107 MG MG A3002 1555 1555 2.15 LINK OD2 ASP A 255 MG MG A3003 1555 1555 2.40 LINK O7 NI9 A3001 MG MG A3002 1555 1555 2.40 LINK O3 NI9 A3001 MG MG A3002 1555 1555 2.43 LINK O7 NI9 A3001 MG MG A3004 1555 1555 2.10 LINK MG MG A3002 O HOH A5225 1555 1555 2.03 LINK MG MG A3003 O HOH A5001 1555 1555 2.40 LINK MG MG A3004 O HOH A5002 1555 1555 1.76 LINK MG MG A3004 O HOH A5003 1555 1555 2.13 LINK OD1 ASP B 103 MG MG B4002 1555 1555 2.09 LINK OD2 ASP B 103 MG MG B4004 1555 1555 2.46 LINK OD2 ASP B 107 MG MG B4002 1555 1555 2.18 LINK OD2 ASP B 107 MG MG B4004 1555 1555 2.40 LINK OD2 ASP B 255 MG MG B4003 1555 1555 2.39 LINK O3 NI9 B4001 MG MG B4002 1555 1555 2.10 LINK O7 NI9 B4001 MG MG B4002 1555 1555 2.31 LINK O6 NI9 B4001 MG MG B4003 1555 1555 2.16 LINK O7 NI9 B4001 MG MG B4004 1555 1555 2.25 LINK MG MG B4003 O HOH B5161 1555 1555 2.40 LINK MG MG B4003 O HOH B5264 1555 1555 2.19 LINK MG MG B4004 O HOH B5004 1555 1555 2.28 SITE 1 AC1 3 ASP A 103 ASP A 107 HOH A5225 SITE 1 AC2 2 ASP A 255 HOH A5001 SITE 1 AC3 5 ASP A 103 ASP A 107 ASP A 175 HOH A5002 SITE 2 AC3 5 HOH A5003 SITE 1 AC4 2 ASP B 103 ASP B 107 SITE 1 AC5 3 ASP B 255 HOH B5161 HOH B5264 SITE 1 AC6 4 ASP B 103 ASP B 107 ASP B 175 HOH B5004 SITE 1 AC7 16 TYR A 99 ASP A 103 ASP A 107 ARG A 112 SITE 2 AC7 16 GLN A 172 LYS A 212 THR A 213 TYR A 216 SITE 3 AC7 16 GLN A 252 ASP A 255 LYS A 269 HOH A5001 SITE 4 AC7 16 HOH A5003 HOH A5060 HOH A5143 HOH A5225 SITE 1 AC8 13 TYR B 99 ASP B 103 ASP B 107 ARG B 112 SITE 2 AC8 13 GLN B 172 LYS B 212 THR B 213 ASP B 255 SITE 3 AC8 13 LYS B 269 HOH B5004 HOH B5116 HOH B5117 SITE 4 AC8 13 HOH B5161 SITE 1 AC9 3 CYS B 159 ARG B 160 ARG B 163 SITE 1 BC1 12 LYS B 47 ARG B 50 GLN B 96 ARG B 113 SITE 2 BC1 12 TYR B 216 PHE B 251 GLN B 252 ASP B 255 SITE 3 BC1 12 ARG B 365 HOH B5045 HOH B5112 HOH B5275 SITE 1 BC2 16 GLY A 46 LYS A 47 ARG A 50 GLN A 96 SITE 2 BC2 16 ARG A 113 TYR A 216 THR A 217 PHE A 251 SITE 3 BC2 16 GLN A 252 ASP A 255 HOH A5006 HOH A5022 SITE 4 BC2 16 HOH A5149 HOH A5151 HOH A5242 HOH A5252 SITE 1 BC3 5 ARG A 163 THR A 167 TYR A 215 HOH A5294 SITE 2 BC3 5 LYS B 24 CRYST1 133.939 117.898 63.274 90.00 111.27 90.00 C 1 2 1 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 0.007466 0.000000 0.002906 0.00000 SCALE2 0.000000 0.008482 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016960 0.00000