PDB Short entry for 2DEM HEADER HYDROLASE/DNA 13-FEB-06 2DEM TITLE CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE IN COMPLEX WITH AP:A TITLE 2 CONTAINING DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*TP*GP*TP*TP*GP*CP*(D1P)P*TP*TP*AP*GP*TP*CP*C)-3'; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*GP*AP*CP*TP*AP*AP*AP*GP*CP*AP*AP*CP*A)-3'; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: URACIL-DNA GLYCOSYLASE; COMPND 11 CHAIN: A; COMPND 12 EC: 3.2.2.-; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 11 ORGANISM_TAXID: 300852; SOURCE 12 STRAIN: HB8; SOURCE 13 GENE: TTUDGB; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS BASE EXCISION REPAIR, URACIL-DNA GLYCOSYLASE, IRON/SULFUR CLUSTER, KEYWDS 2 THERMOPHILE, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON KEYWDS 3 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 4 GENOMICS/PROTEOMICS INITIATIVE, RSGI, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.KOSAKA,N.NAKAGAWA,R.MASUI,J.HOSEKI,S.KURAMITSU,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 8 25-OCT-23 2DEM 1 REMARK REVDAT 7 17-FEB-21 2DEM 1 SOURCE REMARK LINK REVDAT 6 11-OCT-17 2DEM 1 REMARK REVDAT 5 13-JUL-11 2DEM 1 VERSN REVDAT 4 09-JUN-09 2DEM 1 REVDAT REVDAT 3 24-FEB-09 2DEM 1 VERSN REVDAT 2 06-JAN-09 2DEM 1 JRNL REVDAT 1 24-APR-07 2DEM 0 JRNL AUTH H.KOSAKA,J.HOSEKI,N.NAKAGAWA,S.KURAMITSU,R.MASUI JRNL TITL CRYSTAL STRUCTURE OF FAMILY 5 URACIL-DNA GLYCOSYLASE BOUND JRNL TITL 2 TO DNA. JRNL REF J.MOL.BIOL. V. 373 839 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17870091 JRNL DOI 10.1016/J.JMB.2007.08.022 REMARK 2 REMARK 2 RESOLUTION. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.03 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) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 35425 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) : 0.200 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3529 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 562 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1715 REMARK 3 NUCLEIC ACID ATOMS : 581 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 301 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.82000 REMARK 3 B22 (A**2) : 8.42000 REMARK 3 B33 (A**2) : -5.60000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.025 REMARK 3 BOND ANGLES (DEGREES) : 2.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 3.430 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) : 1.130 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.580 ; 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 2DEM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000025326. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.9 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 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS VII REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35480 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 37.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.140 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.06 REMARK 200 R MERGE FOR SHELL (I) : 0.30500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: PDB ENTRY 2DDG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4M NAKPO4, PH 3.9, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 46.70500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.70500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 34.46000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 75.08500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.46000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 75.08500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 46.70500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.46000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 75.08500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 46.70500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.46000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 75.08500 REMARK 290 SMTRY3 8 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 APPLY THE FOLLOWING TO CHAINS: C, D, A 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 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 ARG A 14 36.40 -145.35 REMARK 500 LEU A 58 -62.38 -90.31 REMARK 500 PHE A 72 22.94 49.90 REMARK 500 THR A 110 -167.85 -160.07 REMARK 500 LYS A 119 17.91 58.02 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 DT C 4 0.07 SIDE CHAIN 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 SF4 A 220 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 13 SG REMARK 620 2 SF4 A 220 S1 113.8 REMARK 620 3 SF4 A 220 S2 113.6 103.7 REMARK 620 4 SF4 A 220 S3 114.2 105.4 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 220 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 16 SG REMARK 620 2 SF4 A 220 S1 110.1 REMARK 620 3 SF4 A 220 S3 114.8 105.4 REMARK 620 4 SF4 A 220 S4 116.0 105.0 104.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 220 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 115 SG REMARK 620 2 SF4 A 220 S2 111.0 REMARK 620 3 SF4 A 220 S3 115.6 105.4 REMARK 620 4 SF4 A 220 S4 114.8 104.1 104.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 220 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 130 SG REMARK 620 2 SF4 A 220 S1 114.4 REMARK 620 3 SF4 A 220 S2 117.6 104.4 REMARK 620 4 SF4 A 220 S4 110.1 104.9 104.4 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 SF4 A 220 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2HP A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2HP D 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EOH A 1005 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D3Y RELATED DB: PDB REMARK 900 FREE STRUCTURE REMARK 900 RELATED ID: 2DDG RELATED DB: PDB REMARK 900 COMPLEX WITH AP:G CONTAINING DNA REMARK 900 RELATED ID: TTK003000722.3 RELATED DB: TARGETDB DBREF 2DEM A 1 219 GB 55981118 YP_144415 1 219 DBREF 2DEM C 1 15 PDB 2DEM 2DEM 1 15 DBREF 2DEM D 1 14 PDB 2DEM 2DEM 1 14 SEQRES 1 C 15 DA DT DG DT DT DG DC ORP DT DT DA DG DT SEQRES 2 C 15 DC DC SEQRES 1 D 14 DG DG DA DC DT DA DA DA DG DC DA DA DC SEQRES 2 D 14 DA SEQRES 1 A 219 MET ASP ARG GLU ALA PHE VAL GLN THR LEU THR ALA CYS SEQRES 2 A 219 ARG LEU CYS PRO ARG LEU VAL ALA TRP ARG GLU GLU VAL SEQRES 3 A 219 VAL GLY ARG LYS ARG ALA PHE ARG GLY GLU PRO TYR TRP SEQRES 4 A 219 ALA ARG PRO VAL PRO GLY PHE GLY ASP PRO GLU ALA ARG SEQRES 5 A 219 ILE LEU LEU PHE GLY LEU ALA PRO GLY ALA HIS GLY SER SEQRES 6 A 219 ASN ARG THR GLY ARG PRO PHE THR GLY ASP ALA SER GLY SEQRES 7 A 219 ALA PHE LEU TYR PRO LEU LEU HIS GLU ALA GLY LEU SER SEQRES 8 A 219 SER LYS PRO GLU SER LEU PRO GLY ASP ASP LEU ARG LEU SEQRES 9 A 219 TYR GLY VAL TYR LEU THR ALA ALA VAL ARG CYS ALA PRO SEQRES 10 A 219 PRO LYS ASN LYS PRO THR PRO GLU GLU LEU ARG ALA CYS SEQRES 11 A 219 ALA ARG TRP THR GLU VAL GLU LEU GLY LEU LEU PRO GLU SEQRES 12 A 219 VAL ARG VAL TYR VAL ALA LEU GLY ARG ILE ALA LEU GLU SEQRES 13 A 219 ALA LEU LEU ALA HIS PHE GLY LEU ARG LYS SER ALA HIS SEQRES 14 A 219 PRO PHE ARG HIS GLY ALA HIS TYR PRO LEU PRO GLY GLY SEQRES 15 A 219 ARG HIS LEU LEU ALA SER TYR HIS VAL SER ARG GLN ASN SEQRES 16 A 219 THR GLN THR GLY ARG LEU THR ARG GLU MET PHE LEU GLU SEQRES 17 A 219 VAL LEU MET GLU ALA LYS ARG LEU ALA GLY LEU HET ORP C 8 12 HET 2HP D1002 5 HET SF4 A 220 8 HET 2HP A1001 5 HET GOL A1003 6 HET GOL A1004 6 HET EOH A1005 3 HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE HETNAM 2HP DIHYDROGENPHOSPHATE ION HETNAM SF4 IRON/SULFUR CLUSTER HETNAM GOL GLYCEROL HETNAM EOH ETHANOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 ORP C5 H11 O7 P FORMUL 4 2HP 2(H2 O4 P 1-) FORMUL 5 SF4 FE4 S4 FORMUL 7 GOL 2(C3 H8 O3) FORMUL 9 EOH C2 H6 O FORMUL 10 HOH *301(H2 O) HELIX 1 1 ASP A 2 ALA A 12 1 11 HELIX 2 2 CYS A 16 VAL A 26 1 11 HELIX 3 3 LYS A 30 ARG A 34 5 5 HELIX 4 4 GLY A 64 GLY A 69 1 6 HELIX 5 5 ASP A 75 ALA A 88 1 14 HELIX 6 6 PRO A 117 LYS A 121 5 5 HELIX 7 7 THR A 123 LEU A 140 1 18 HELIX 8 8 GLY A 151 PHE A 162 1 12 HELIX 9 9 ARG A 165 HIS A 169 5 5 HELIX 10 10 SER A 192 GLN A 197 1 6 HELIX 11 11 THR A 202 GLY A 218 1 17 SHEET 1 A 6 PHE A 46 GLY A 47 0 SHEET 2 A 6 VAL A 107 ALA A 111 -1 O LEU A 109 N PHE A 46 SHEET 3 A 6 ILE A 53 GLY A 57 1 N GLY A 57 O THR A 110 SHEET 4 A 6 VAL A 146 LEU A 150 1 O VAL A 148 N PHE A 56 SHEET 5 A 6 ARG A 183 SER A 188 1 O LEU A 186 N ALA A 149 SHEET 6 A 6 HIS A 176 LEU A 179 -1 N TYR A 177 O LEU A 185 LINK O3' DC C 7 P ORP C 8 1555 1555 1.59 LINK O3 ORP C 8 P DT C 9 1555 1555 1.59 LINK SG CYS A 13 FE4 SF4 A 220 1555 1555 2.39 LINK SG CYS A 16 FE2 SF4 A 220 1555 1555 2.52 LINK SG CYS A 115 FE1 SF4 A 220 1555 1555 2.45 LINK SG CYS A 130 FE3 SF4 A 220 1555 1555 2.44 SITE 1 AC1 6 CYS A 13 LEU A 15 CYS A 16 LEU A 19 SITE 2 AC1 6 CYS A 115 CYS A 130 SITE 1 AC2 9 ALA A 59 PRO A 60 GLY A 61 SER A 65 SITE 2 AC2 9 PHE A 72 ASP A 75 HOH A1056 HOH A1077 SITE 3 AC2 9 ORP C 8 SITE 1 AC3 5 ARG A 31 GLU A 50 HOH A1229 DC D 13 SITE 2 AC3 5 DA D 14 SITE 1 AC4 6 PHE A 72 THR A 73 GLY A 74 ASP A 75 SITE 2 AC4 6 GLU A 95 SER A 96 SITE 1 AC5 8 PRO A 37 TYR A 38 LEU A 84 GLU A 87 SITE 2 AC5 8 ARG A 203 HOH A1015 HOH A1086 HOH A1143 SITE 1 AC6 4 THR A 202 ARG A 203 HOH A1137 HOH A1165 CRYST1 68.920 150.170 93.410 90.00 90.00 90.00 C 2 2 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 0.014510 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006659 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010705 0.00000