HEADER TRANSFERASE 27-JUL-08 3DYG TITLE T. BRUCEI FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH BISPHOSPHONATE TITLE 2 BPH-461 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 30-AUG-23 3DYG 1 REMARK SEQADV LINK REVDAT 1 05-MAY-09 3DYG 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. 2.10 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 58133.500 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 51405 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) : 0.207 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1533 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 9 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5192 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 2.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 155 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5742 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 561 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.05000 REMARK 3 B22 (A**2) : -5.78000 REMARK 3 B33 (A**2) : 1.73000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.89000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.21 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) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.240 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.830 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) : 1.700 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.350 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.630 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.510 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 55.43 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 3DYG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000048646. 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 : 53536 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 0.1010 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 (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 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: PDB ENTRY 2EWG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 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 67.78250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.26000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.78250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 59.26000 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: 9820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -116.0 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 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 181 107.76 -52.47 REMARK 500 THR A 213 -50.39 -124.02 REMARK 500 ASP A 306 109.29 -53.70 REMARK 500 SER B 63 -19.10 177.61 REMARK 500 ASP B 181 108.90 -58.28 REMARK 500 LEU B 185 106.12 -57.86 REMARK 500 PHE B 197 29.68 46.06 REMARK 500 THR B 213 -51.79 -127.88 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 74.5 REMARK 620 3 NI9 A3001 O3 135.4 146.5 REMARK 620 4 NI9 A3001 O7 87.6 74.2 90.3 REMARK 620 5 HOH A5003 O 73.9 76.9 120.4 148.9 REMARK 620 6 HOH A5516 O 152.4 79.5 72.2 94.3 91.3 REMARK 620 N 1 2 3 4 5 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 ASP A 107 OD2 77.1 REMARK 620 3 NI9 A3001 O7 90.2 70.3 REMARK 620 4 HOH A5005 O 91.3 112.8 176.8 REMARK 620 5 HOH A5006 O 166.6 89.5 85.8 93.4 REMARK 620 6 HOH A5014 O 98.4 165.0 95.6 81.4 94.6 REMARK 620 N 1 2 3 4 5 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 NI9 A3001 O6 102.3 REMARK 620 3 HOH A5001 O 156.8 86.9 REMARK 620 4 HOH A5002 O 87.7 159.2 77.5 REMARK 620 5 HOH A5012 O 80.6 88.3 78.4 75.1 REMARK 620 N 1 2 3 4 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 OD2 REMARK 620 2 ASP B 107 OD2 81.4 REMARK 620 3 NI9 B4001 O7 91.5 75.7 REMARK 620 4 HOH B5004 O 85.7 100.5 175.6 REMARK 620 5 HOH B5082 O 166.3 84.9 84.4 97.5 REMARK 620 N 1 2 3 4 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 OD1 REMARK 620 2 ASP B 107 OD2 76.8 REMARK 620 3 NI9 B4001 O7 95.4 75.6 REMARK 620 4 HOH B5007 O 84.3 104.3 179.7 REMARK 620 5 HOH B5008 O 175.3 99.1 85.8 94.5 REMARK 620 6 HOH B5009 O 94.5 168.6 98.2 81.8 89.8 REMARK 620 N 1 2 3 4 5 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 99.3 REMARK 620 3 HOH B5010 O 110.8 149.4 REMARK 620 4 HOH B5015 O 90.7 87.5 86.6 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 ACT A 8001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 8002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI9 A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI9 B 4001 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 9001 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME B 9002 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 7001 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 7002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EWG RELATED DB: PDB REMARK 900 RELATED ID: 2I19 RELATED DB: PDB REMARK 900 RELATED ID: 2OGD RELATED DB: PDB REMARK 900 RELATED ID: 3DYF RELATED DB: PDB REMARK 900 RELATED ID: 3DYH RELATED DB: PDB DBREF 3DYG A 1 367 UNP Q86C09 Q86C09_9TRYP 1 367 DBREF 3DYG B 1 367 UNP Q86C09 Q86C09_9TRYP 1 367 SEQADV 3DYG MET A -22 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG GLY A -21 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG SER A -20 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG SER A -19 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG HIS A -18 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG HIS A -17 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG HIS A -16 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG HIS A -15 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG HIS A -14 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG HIS A -13 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG SER A -12 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG SER A -11 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG GLY A -10 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG LEU A -9 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG VAL A -8 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG PRO A -7 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG ARG A -6 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG GLY A -5 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG SER A -4 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG HIS A -3 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG MET A -2 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG ALA A -1 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG SER A 0 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG MET B -22 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG GLY B -21 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG SER B -20 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG SER B -19 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG HIS B -18 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG HIS B -17 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG HIS B -16 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG HIS B -15 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG HIS B -14 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG HIS B -13 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG SER B -12 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG SER B -11 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG GLY B -10 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG LEU B -9 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG VAL B -8 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG PRO B -7 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG ARG B -6 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG GLY B -5 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG SER B -4 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG HIS B -3 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG MET B -2 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG ALA B -1 UNP Q86C09 EXPRESSION TAG SEQADV 3DYG 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 BME A9001 4 HET MPD A7001 8 HET MG B4002 1 HET MG B4003 1 HET MG B4004 1 HET ACT B8002 4 HET NI9 B4001 18 HET BME B9002 4 HET MPD B7002 8 HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM NI9 3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM HETNAM BME BETA-MERCAPTOETHANOL HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 MG 6(MG 2+) FORMUL 6 ACT 2(C2 H3 O2 1-) FORMUL 7 NI9 2(C7 H11 F N O7 P2 1+) FORMUL 8 BME 2(C2 H6 O S) FORMUL 9 MPD 2(C6 H14 O2) FORMUL 17 HOH *561(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 62 1 15 HELIX 4 4 GLY A 75 ASN A 108 1 34 HELIX 5 5 TRP A 118 HIS A 121 5 4 HELIX 6 6 THR A 125 ALA A 149 1 25 HELIX 7 7 PHE A 153 THR A 177 1 25 HELIX 8 8 ASP A 181 LEU A 185 5 5 HELIX 9 9 THR A 201 THR A 213 1 13 HELIX 10 10 THR A 213 TYR A 218 1 6 HELIX 11 11 TYR A 218 SER A 229 1 12 HELIX 12 12 ALA A 231 VAL A 235 5 5 HELIX 13 13 ASP A 236 THR A 262 1 27 HELIX 14 14 PRO A 263 GLY A 268 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 ALA A 320 1 15 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 61 1 14 HELIX 23 23 GLY B 75 ASN B 108 1 34 HELIX 24 24 TRP B 118 HIS B 121 5 4 HELIX 25 25 THR B 125 ALA B 149 1 25 HELIX 26 26 PHE B 153 THR B 177 1 25 HELIX 27 27 ASP B 181 LEU B 185 5 5 HELIX 28 28 THR B 201 THR B 213 1 13 HELIX 29 29 THR B 213 TYR B 218 1 6 HELIX 30 30 TYR B 218 SER B 229 1 12 HELIX 31 31 ALA B 231 VAL B 235 5 5 HELIX 32 32 ASP B 236 THR B 262 1 27 HELIX 33 33 PRO B 263 GLY B 268 1 6 HELIX 34 34 SER B 280 ALA B 290 1 11 HELIX 35 35 SER B 291 ALA B 300 1 10 HELIX 36 36 ASP B 306 ALA B 320 1 15 HELIX 37 37 ASP B 321 LEU B 346 1 26 HELIX 38 38 SER B 348 TYR B 363 1 16 SHEET 1 A 2 THR A 111 ARG A 112 0 SHEET 2 A 2 LYS A 115 PRO A 116 -1 O LYS A 115 N ARG A 112 SHEET 1 B 2 THR B 111 ARG B 112 0 SHEET 2 B 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 2.10 LINK OD1 ASP A 103 MG MG A3004 1555 1555 2.09 LINK OD2 ASP A 107 MG MG A3002 1555 1555 2.28 LINK OD2 ASP A 107 MG MG A3004 1555 1555 2.36 LINK OD2 ASP A 255 MG MG A3003 1555 1555 2.18 LINK O3 NI9 A3001 MG MG A3002 1555 1555 2.11 LINK O7 NI9 A3001 MG MG A3002 1555 1555 2.08 LINK O6 NI9 A3001 MG MG A3003 1555 1555 2.06 LINK O7 NI9 A3001 MG MG A3004 1555 1555 2.21 LINK MG MG A3002 O HOH A5003 1555 1555 2.09 LINK MG MG A3002 O HOH A5516 1555 1555 2.20 LINK MG MG A3003 O HOH A5001 1555 1555 2.25 LINK MG MG A3003 O HOH A5002 1555 1555 2.20 LINK MG MG A3003 O HOH A5012 1555 1555 2.44 LINK MG MG A3004 O HOH A5005 1555 1555 1.98 LINK MG MG A3004 O HOH A5006 1555 1555 1.83 LINK MG MG A3004 O HOH A5014 1555 1555 2.15 LINK OD2 ASP B 103 MG MG B4002 1555 1555 2.02 LINK OD1 ASP B 103 MG MG B4004 1555 1555 2.06 LINK OD2 ASP B 107 MG MG B4002 1555 1555 2.10 LINK OD2 ASP B 107 MG MG B4004 1555 1555 2.10 LINK OD2 ASP B 255 MG MG B4003 1555 1555 1.92 LINK O7 NI9 B4001 MG MG B4002 1555 1555 2.19 LINK O6 NI9 B4001 MG MG B4003 1555 1555 2.24 LINK O7 NI9 B4001 MG MG B4004 1555 1555 2.20 LINK MG MG B4002 O HOH B5004 1555 1555 1.94 LINK MG MG B4002 O HOH B5082 1555 1555 2.18 LINK MG MG B4003 O HOH B5010 1555 1555 2.13 LINK MG MG B4003 O HOH B5015 1555 1555 2.21 LINK MG MG B4004 O HOH B5007 1555 1555 1.95 LINK MG MG B4004 O HOH B5008 1555 1555 1.93 LINK MG MG B4004 O HOH B5009 1555 1555 2.08 SITE 1 AC1 4 ASP A 103 ASP A 107 HOH A5003 HOH A5516 SITE 1 AC2 5 ASP A 255 LYS A 269 HOH A5001 HOH A5002 SITE 2 AC2 5 HOH A5012 SITE 1 AC3 5 ASP A 103 ASP A 107 HOH A5005 HOH A5006 SITE 2 AC3 5 HOH A5014 SITE 1 AC4 4 ASP B 103 ASP B 107 HOH B5004 HOH B5082 SITE 1 AC5 4 ASP B 255 HOH B5010 HOH B5015 HOH B5298 SITE 1 AC6 5 ASP B 103 ASP B 107 HOH B5007 HOH B5008 SITE 2 AC6 5 HOH B5009 SITE 1 AC7 8 GLY A 46 LYS A 47 GLN A 96 ARG A 113 SITE 2 AC7 8 LYS A 367 HOH A5016 HOH A5035 HOH A5477 SITE 1 AC8 8 LYS B 47 ARG B 50 GLN B 96 ARG B 113 SITE 2 AC8 8 HOH B5063 HOH B5176 HOH B5201 HOH B5341 SITE 1 AC9 17 TYR A 99 ASP A 103 ASP A 107 ARG A 112 SITE 2 AC9 17 GLN A 172 LYS A 212 THR A 213 ASP A 255 SITE 3 AC9 17 LYS A 269 HOH A5001 HOH A5006 HOH A5014 SITE 4 AC9 17 HOH A5081 HOH A5113 HOH A5252 HOH A5516 SITE 5 AC9 17 HOH A5551 SITE 1 BC1 17 TYR B 99 ASP B 103 ASP B 107 ARG B 112 SITE 2 BC1 17 GLN B 172 LYS B 212 THR B 213 ASP B 255 SITE 3 BC1 17 LYS B 269 HOH B5008 HOH B5009 HOH B5013 SITE 4 BC1 17 HOH B5015 HOH B5082 HOH B5184 HOH B5185 SITE 5 BC1 17 HOH B5298 SITE 1 BC2 3 ASP A 156 CYS A 159 ARG A 160 SITE 1 BC3 3 CYS B 159 ARG B 160 ARG B 163 SITE 1 BC4 6 ARG A 163 TYR A 215 GLU A 241 HOH A5023 SITE 2 BC4 6 HOH A5440 LYS B 24 SITE 1 BC5 5 LYS A 24 PHE A 25 ARG B 163 THR B 167 SITE 2 BC5 5 TYR B 215 CRYST1 135.565 118.520 63.186 90.00 112.36 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 0.007377 0.000000 0.003035 0.00000 SCALE2 0.000000 0.008437 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017113 0.00000