PDB Short entry for 3IKE HEADER LYASE 05-AUG-09 3IKE TITLE CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE TITLE 2 SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI WITH CYTOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: MECPS, MECDP-SYNTHASE; COMPND 5 EC: 4.6.1.12; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA PSEUDOMALLEI; SOURCE 3 ORGANISM_COMMON: PSEUDOMONAS PSEUDOMALLEI; SOURCE 4 ORGANISM_TAXID: 28450; SOURCE 5 STRAIN: 1710B; SOURCE 6 GENE: ISPF, MECS, BPSL2098; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: AVA0421 KEYWDS NIAID, SSGCID, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS KEYWDS 2 DISEASE, FRAGMENT, ISOPRENE BIOSYNTHESIS, LYASE, METAL-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 5 06-SEP-23 3IKE 1 REMARK SEQADV LINK REVDAT 4 01-NOV-17 3IKE 1 REMARK REVDAT 3 30-OCT-13 3IKE 1 REMARK REVDAT 2 13-JUL-11 3IKE 1 JRNL REVDAT 1 18-AUG-09 3IKE 0 JRNL AUTH D.W.BEGLEY,R.C.HARTLEY,D.R.DAVIES,T.E.EDWARDS,J.T.LEONARD, JRNL AUTH 2 J.ABENDROTH,C.A.BURRIS,J.BHANDARI,P.J.MYLER,B.L.STAKER, JRNL AUTH 3 L.J.STEWART JRNL TITL LEVERAGING STRUCTURE DETERMINATION WITH FRAGMENT SCREENING JRNL TITL 2 FOR INFECTIOUS DISEASE DRUG TARGETS: MECP SYNTHASE FROM JRNL TITL 3 BURKHOLDERIA PSEUDOMALLEI. JRNL REF J STRUCT FUNCT GENOMICS V. 12 63 2011 JRNL REFN JRNL PMID 21359640 JRNL DOI 10.1007/S10969-011-9102-6 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.BAUGH,L.A.GALLAGHER,R.PATRAPUVICH,M.C.CLIFTON, REMARK 1 AUTH 2 A.S.GARDBERG,T.E.EDWARDS,B.ARMOUR,D.W.BEGLEY,S.H.DIETERICH, REMARK 1 AUTH 3 D.M.DRANOW,J.ABENDROTH,J.W.FAIRMAN,D.FOX,B.L.STAKER,I.PHAN, REMARK 1 AUTH 4 A.GILLESPIE,R.CHOI,S.NAKAZAWA-HEWITT,M.T.NGUYEN,A.NAPULI, REMARK 1 AUTH 5 L.BARRETT,G.W.BUCHKO,R.STACY,P.J.MYLER,L.J.STEWART,C.MANOIL, REMARK 1 AUTH 6 W.C.VAN VOORHIS REMARK 1 TITL COMBINING FUNCTIONAL AND STRUCTURAL GENOMICS TO SAMPLE THE REMARK 1 TITL 2 ESSENTIAL BURKHOLDERIA STRUCTOME. REMARK 1 REF PLOS ONE V. 8 53851 2013 REMARK 1 REFN ESSN 1932-6203 REMARK 1 PMID 23382856 REMARK 1 DOI 10.1371/JOURNAL.PONE.0053851 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21111 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 + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1084 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1462 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3398 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 241 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.36000 REMARK 3 B22 (A**2) : 1.62000 REMARK 3 B33 (A**2) : -0.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.14000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.358 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.235 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.311 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3472 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4704 ; 1.442 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 453 ; 5.780 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;31.953 ;22.800 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 538 ;15.073 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;18.757 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 544 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2656 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2264 ; 0.816 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3575 ; 1.473 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1208 ; 2.161 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1129 ; 3.438 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3IKE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054521. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21121 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3F0E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M MG FORMATE, 34.4 REMARK 280 MG/ML PROTEIN, 0.4/0.4 UL DROPS, CRYSTAL TRACKING ID 204112A1, REMARK 280 PH 5.9, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 58.82950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.03200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.82950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.03200 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -135.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 194 LIES ON A SPECIAL POSITION. 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 GLY A -3 REMARK 465 PRO A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLU A 159 REMARK 465 ALA A 160 REMARK 465 ALA A 161 REMARK 465 ALA A 162 REMARK 465 GLY B -3 REMARK 465 PRO B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 GLY B 35 REMARK 465 HIS B 36 REMARK 465 SER B 37 REMARK 465 LYS B 71 REMARK 465 GLY B 72 REMARK 465 GLU B 159 REMARK 465 ALA B 160 REMARK 465 ALA B 161 REMARK 465 ALA B 162 REMARK 465 GLY C -3 REMARK 465 PRO C -2 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 SER C 64 REMARK 465 ASP C 65 REMARK 465 THR C 66 REMARK 465 ASP C 67 REMARK 465 PRO C 68 REMARK 465 ARG C 69 REMARK 465 PHE C 70 REMARK 465 LYS C 71 REMARK 465 GLY C 72 REMARK 465 ALA C 73 REMARK 465 GLU C 159 REMARK 465 ALA C 160 REMARK 465 ALA C 161 REMARK 465 ALA C 162 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 CG SD CE REMARK 470 LYS A 71 CG CD CE NZ REMARK 470 GLU B 30 CG CD OE1 OE2 REMARK 470 ASP B 65 CG OD1 OD2 REMARK 470 THR B 66 OG1 CG2 REMARK 470 ASP B 67 CG OD1 OD2 REMARK 470 ARG B 69 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 106 CG CD CE NZ REMARK 470 ARG B 158 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 30 CG CD OE1 OE2 REMARK 470 HIS C 36 CG ND1 CD2 CE1 NE2 REMARK 470 LYS C 106 CG CD CE NZ 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 O HOH A 234 O HOH C 206 2.19 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 ASP A 38 2.99 -65.86 REMARK 500 ASP B 2 73.59 -110.42 REMARK 500 ASP B 65 15.99 -62.17 REMARK 500 THR B 66 -74.34 -122.54 REMARK 500 ASP B 67 126.74 -19.58 REMARK 500 ASP C 2 77.91 -101.45 REMARK 500 SER C 37 -156.45 -98.24 REMARK 500 ASP C 38 3.47 -68.85 REMARK 500 ASP C 40 92.32 -64.78 REMARK 500 LYS C 138 17.66 57.01 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 10 OD2 REMARK 620 2 HIS A 12 NE2 92.6 REMARK 620 3 HIS A 44 ND1 99.4 113.7 REMARK 620 4 HOH B 212 O 114.9 117.9 114.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 163 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 188 O REMARK 620 2 HOH B 219 O 105.4 REMARK 620 3 HOH C 187 O 97.4 121.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 10 OD2 REMARK 620 2 HIS B 12 NE2 108.5 REMARK 620 3 HIS B 44 ND1 91.1 130.3 REMARK 620 4 HOH C 186 O 111.6 103.3 111.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 10 OD2 REMARK 620 2 HIS C 12 NE2 102.2 REMARK 620 3 HIS C 44 ND1 99.7 119.9 REMARK 620 4 HOH C 226 O 118.8 109.5 107.1 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 ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CYT A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CYT B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CYT C 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3F0D RELATED DB: PDB REMARK 900 HIGH RESOLUTION APO STRUCTURE FROM A DIFFERENT CRYSTAL FORM REMARK 900 RELATED ID: 3F0E RELATED DB: PDB REMARK 900 APO STRUCTURE IN SAME CRYSTAL FORM REMARK 900 RELATED ID: 3F0F RELATED DB: PDB REMARK 900 STRUCTURE WITH HYDROLYZED CDP REMARK 900 RELATED ID: 3F0G RELATED DB: PDB REMARK 900 STRUCTURE WITH CMP REMARK 900 RELATED ID: 3IEW RELATED DB: PDB REMARK 900 STRUCTURE WITH CTP REMARK 900 RELATED ID: 3IEQ RELATED DB: PDB REMARK 900 STRUCTURE WITH CYTIDINE REMARK 900 RELATED ID: 3IKF RELATED DB: PDB REMARK 900 RELATED ID: BUPSA.00122.A RELATED DB: TARGETDB DBREF 3IKE A 1 162 UNP Q63T71 ISPF_BURPS 1 162 DBREF 3IKE B 1 162 UNP Q63T71 ISPF_BURPS 1 162 DBREF 3IKE C 1 162 UNP Q63T71 ISPF_BURPS 1 162 SEQADV 3IKE GLY A -3 UNP Q63T71 EXPRESSION TAG SEQADV 3IKE PRO A -2 UNP Q63T71 EXPRESSION TAG SEQADV 3IKE GLY A -1 UNP Q63T71 EXPRESSION TAG SEQADV 3IKE SER A 0 UNP Q63T71 EXPRESSION TAG SEQADV 3IKE GLY B -3 UNP Q63T71 EXPRESSION TAG SEQADV 3IKE PRO B -2 UNP Q63T71 EXPRESSION TAG SEQADV 3IKE GLY B -1 UNP Q63T71 EXPRESSION TAG SEQADV 3IKE SER B 0 UNP Q63T71 EXPRESSION TAG SEQADV 3IKE GLY C -3 UNP Q63T71 EXPRESSION TAG SEQADV 3IKE PRO C -2 UNP Q63T71 EXPRESSION TAG SEQADV 3IKE GLY C -1 UNP Q63T71 EXPRESSION TAG SEQADV 3IKE SER C 0 UNP Q63T71 EXPRESSION TAG SEQRES 1 A 166 GLY PRO GLY SER MET ASP PHE ARG ILE GLY GLN GLY TYR SEQRES 2 A 166 ASP VAL HIS GLN LEU VAL PRO GLY ARG PRO LEU ILE ILE SEQRES 3 A 166 GLY GLY VAL THR ILE PRO TYR GLU ARG GLY LEU LEU GLY SEQRES 4 A 166 HIS SER ASP ALA ASP VAL LEU LEU HIS ALA ILE THR ASP SEQRES 5 A 166 ALA LEU PHE GLY ALA ALA ALA LEU GLY ASP ILE GLY ARG SEQRES 6 A 166 HIS PHE SER ASP THR ASP PRO ARG PHE LYS GLY ALA ASP SEQRES 7 A 166 SER ARG ALA LEU LEU ARG GLU CYS ALA SER ARG VAL ALA SEQRES 8 A 166 GLN ALA GLY PHE ALA ILE ARG ASN VAL ASP SER THR ILE SEQRES 9 A 166 ILE ALA GLN ALA PRO LYS LEU ALA PRO HIS ILE ASP ALA SEQRES 10 A 166 MET ARG ALA ASN ILE ALA ALA ASP LEU ASP LEU PRO LEU SEQRES 11 A 166 ASP ARG VAL ASN VAL LYS ALA LYS THR ASN GLU LYS LEU SEQRES 12 A 166 GLY TYR LEU GLY ARG GLY GLU GLY ILE GLU ALA GLN ALA SEQRES 13 A 166 ALA ALA LEU VAL VAL ARG GLU ALA ALA ALA SEQRES 1 B 166 GLY PRO GLY SER MET ASP PHE ARG ILE GLY GLN GLY TYR SEQRES 2 B 166 ASP VAL HIS GLN LEU VAL PRO GLY ARG PRO LEU ILE ILE SEQRES 3 B 166 GLY GLY VAL THR ILE PRO TYR GLU ARG GLY LEU LEU GLY SEQRES 4 B 166 HIS SER ASP ALA ASP VAL LEU LEU HIS ALA ILE THR ASP SEQRES 5 B 166 ALA LEU PHE GLY ALA ALA ALA LEU GLY ASP ILE GLY ARG SEQRES 6 B 166 HIS PHE SER ASP THR ASP PRO ARG PHE LYS GLY ALA ASP SEQRES 7 B 166 SER ARG ALA LEU LEU ARG GLU CYS ALA SER ARG VAL ALA SEQRES 8 B 166 GLN ALA GLY PHE ALA ILE ARG ASN VAL ASP SER THR ILE SEQRES 9 B 166 ILE ALA GLN ALA PRO LYS LEU ALA PRO HIS ILE ASP ALA SEQRES 10 B 166 MET ARG ALA ASN ILE ALA ALA ASP LEU ASP LEU PRO LEU SEQRES 11 B 166 ASP ARG VAL ASN VAL LYS ALA LYS THR ASN GLU LYS LEU SEQRES 12 B 166 GLY TYR LEU GLY ARG GLY GLU GLY ILE GLU ALA GLN ALA SEQRES 13 B 166 ALA ALA LEU VAL VAL ARG GLU ALA ALA ALA SEQRES 1 C 166 GLY PRO GLY SER MET ASP PHE ARG ILE GLY GLN GLY TYR SEQRES 2 C 166 ASP VAL HIS GLN LEU VAL PRO GLY ARG PRO LEU ILE ILE SEQRES 3 C 166 GLY GLY VAL THR ILE PRO TYR GLU ARG GLY LEU LEU GLY SEQRES 4 C 166 HIS SER ASP ALA ASP VAL LEU LEU HIS ALA ILE THR ASP SEQRES 5 C 166 ALA LEU PHE GLY ALA ALA ALA LEU GLY ASP ILE GLY ARG SEQRES 6 C 166 HIS PHE SER ASP THR ASP PRO ARG PHE LYS GLY ALA ASP SEQRES 7 C 166 SER ARG ALA LEU LEU ARG GLU CYS ALA SER ARG VAL ALA SEQRES 8 C 166 GLN ALA GLY PHE ALA ILE ARG ASN VAL ASP SER THR ILE SEQRES 9 C 166 ILE ALA GLN ALA PRO LYS LEU ALA PRO HIS ILE ASP ALA SEQRES 10 C 166 MET ARG ALA ASN ILE ALA ALA ASP LEU ASP LEU PRO LEU SEQRES 11 C 166 ASP ARG VAL ASN VAL LYS ALA LYS THR ASN GLU LYS LEU SEQRES 12 C 166 GLY TYR LEU GLY ARG GLY GLU GLY ILE GLU ALA GLN ALA SEQRES 13 C 166 ALA ALA LEU VAL VAL ARG GLU ALA ALA ALA HET ZN A 201 1 HET CYT A 901 8 HET CL A 163 1 HET MG B 163 1 HET CYT B 901 8 HET ZN B 201 1 HET CYT C 901 8 HET ZN C 201 1 HETNAM ZN ZINC ION HETNAM CYT 6-AMINOPYRIMIDIN-2(1H)-ONE HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETSYN CYT CYTOSINE FORMUL 4 ZN 3(ZN 2+) FORMUL 5 CYT 3(C4 H5 N3 O) FORMUL 6 CL CL 1- FORMUL 7 MG MG 2+ FORMUL 12 HOH *241(H2 O) HELIX 1 1 ASP A 40 ALA A 54 1 15 HELIX 2 2 ASP A 58 PHE A 63 1 6 HELIX 3 3 ASP A 67 LYS A 71 5 5 HELIX 4 4 ASP A 74 ALA A 89 1 16 HELIX 5 5 LEU A 107 PRO A 109 5 3 HELIX 6 6 HIS A 110 ASP A 123 1 14 HELIX 7 7 PRO A 125 VAL A 129 5 5 HELIX 8 8 LEU A 139 ARG A 144 1 6 HELIX 9 9 ASP B 40 ALA B 55 1 16 HELIX 10 10 ASP B 58 PHE B 63 1 6 HELIX 11 11 ASP B 74 ALA B 89 1 16 HELIX 12 12 LEU B 107 PRO B 109 5 3 HELIX 13 13 HIS B 110 ASP B 123 1 14 HELIX 14 14 PRO B 125 VAL B 129 5 5 HELIX 15 15 LEU B 139 ARG B 144 1 6 HELIX 16 16 ASP C 40 ALA C 54 1 15 HELIX 17 17 ASP C 58 PHE C 63 1 6 HELIX 18 18 ASP C 74 ALA C 89 1 16 HELIX 19 19 LEU C 107 PRO C 109 5 3 HELIX 20 20 HIS C 110 LEU C 122 1 13 HELIX 21 21 PRO C 125 VAL C 129 5 5 HELIX 22 22 LEU C 139 ARG C 144 1 6 SHEET 1 A 5 ARG A 31 LEU A 33 0 SHEET 2 A 5 PHE A 3 PRO A 16 -1 N VAL A 15 O GLY A 32 SHEET 3 A 5 GLY A 147 VAL A 157 -1 O ALA A 150 N ASP A 10 SHEET 4 A 5 ALA A 92 ILE A 101 -1 N ARG A 94 O LEU A 155 SHEET 5 A 5 LYS A 132 LYS A 134 1 O LYS A 134 N ILE A 100 SHEET 1 B 2 LEU A 20 ILE A 22 0 SHEET 2 B 2 VAL A 25 ILE A 27 -1 O ILE A 27 N LEU A 20 SHEET 1 C 5 GLY B 32 LEU B 33 0 SHEET 2 C 5 PHE B 3 VAL B 15 -1 N VAL B 15 O GLY B 32 SHEET 3 C 5 GLY B 147 VAL B 157 -1 O ALA B 152 N GLY B 8 SHEET 4 C 5 ALA B 92 ILE B 101 -1 N ILE B 101 O GLU B 149 SHEET 5 C 5 LYS B 132 LYS B 134 1 O LYS B 134 N ILE B 100 SHEET 1 D 2 LEU B 20 ILE B 22 0 SHEET 2 D 2 VAL B 25 ILE B 27 -1 O ILE B 27 N LEU B 20 SHEET 1 E 5 ARG C 31 LEU C 34 0 SHEET 2 E 5 PHE C 3 PRO C 16 -1 N VAL C 15 O GLY C 32 SHEET 3 E 5 GLY C 147 VAL C 157 -1 O ALA C 152 N GLY C 8 SHEET 4 E 5 ALA C 92 ILE C 101 -1 N ILE C 101 O GLU C 149 SHEET 5 E 5 LYS C 132 LYS C 134 1 O LYS C 134 N ILE C 100 SHEET 1 F 2 LEU C 20 ILE C 22 0 SHEET 2 F 2 VAL C 25 ILE C 27 -1 O ILE C 27 N LEU C 20 LINK OD2 ASP A 10 ZN ZN A 201 1555 1555 2.10 LINK NE2 HIS A 12 ZN ZN A 201 1555 1555 2.00 LINK ND1 HIS A 44 ZN ZN A 201 1555 1555 2.04 LINK O HOH A 188 MG MG B 163 1555 1555 2.50 LINK ZN ZN A 201 O HOH B 212 1555 1555 2.17 LINK OD2 ASP B 10 ZN ZN B 201 1555 1555 2.24 LINK NE2 HIS B 12 ZN ZN B 201 1555 1555 1.82 LINK ND1 HIS B 44 ZN ZN B 201 1555 1555 2.02 LINK MG MG B 163 O HOH B 219 1555 1555 2.14 LINK MG MG B 163 O HOH C 187 1555 1555 2.48 LINK ZN ZN B 201 O HOH C 186 1555 1555 2.36 LINK OD2 ASP C 10 ZN ZN C 201 1555 1555 2.05 LINK NE2 HIS C 12 ZN ZN C 201 1555 1555 1.92 LINK ND1 HIS C 44 ZN ZN C 201 1555 1555 1.97 LINK ZN ZN C 201 O HOH C 226 1555 1555 2.22 CISPEP 1 ALA A 104 PRO A 105 0 -3.27 CISPEP 2 ALA B 104 PRO B 105 0 -6.61 CISPEP 3 ALA C 104 PRO C 105 0 3.86 SITE 1 AC1 4 ASP A 10 HIS A 12 HIS A 44 HOH B 212 SITE 1 AC2 7 ALA A 102 PRO A 105 LYS A 106 LEU A 107 SITE 2 AC2 7 ALA A 108 LYS A 134 THR A 135 SITE 1 AC3 5 GLN A 103 THR A 135 ASN A 136 LYS A 138 SITE 2 AC3 5 GLY A 143 SITE 1 AC4 3 HOH A 188 HOH B 219 HOH C 187 SITE 1 AC5 7 ALA B 102 PRO B 105 LYS B 106 LEU B 107 SITE 2 AC5 7 ALA B 108 LYS B 134 THR B 135 SITE 1 AC6 4 ASP B 10 HIS B 12 HIS B 44 HOH C 186 SITE 1 AC7 6 ALA C 102 PRO C 105 LYS C 106 LEU C 107 SITE 2 AC7 6 ALA C 108 LYS C 134 SITE 1 AC8 4 ASP C 10 HIS C 12 HIS C 44 HOH C 226 CRYST1 117.659 68.064 60.156 90.00 96.29 90.00 C 1 2 1 12 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 0.008499 0.000000 0.000937 0.00000 SCALE2 0.000000 0.014692 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016724 0.00000