HEADER DNA 09-FEB-06 2FZA TITLE CRYSTAL STRUCTURE OF D(GCGGGAGC): THE BASE-INTERCALATED DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS BASE-INTERCALATED DUPLEX, BASE-INTERCALATED MOTIF, SHEARED G:A PAIR, KEYWDS 2 DNA, DNA HEXAPLEX, DEOXYRIBONUCLEIC ACID EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,T.CIENGSHIN,E.C.M.JUAN,K.MITOMI,A.TAKENAKA REVDAT 4 13-MAR-24 2FZA 1 REMARK LINK REVDAT 3 18-OCT-17 2FZA 1 REMARK REVDAT 2 24-FEB-09 2FZA 1 VERSN REVDAT 1 23-JAN-07 2FZA 0 JRNL AUTH J.KONDO,T.CIENGSHIN,E.C.M.JUAN,Y.SATO,K.MITOMI,S.SHIMIZU, JRNL AUTH 2 A.TAKENAKA JRNL TITL CRYSTAL STRUCTURE OF D(GCGXGAGC) WITH X=G: A MUTATION AT X JRNL TITL 2 IS POSSIBLE TO OCCUR IN A BASE-INTERCALATED DUPLEX FOR JRNL TITL 3 MULTIPLEX FORMATION JRNL REF NUCLEOSIDES NUCLEOTIDES V. 25 693 2006 JRNL REF 2 NUCLEIC ACIDS JRNL REFN ISSN 1525-7770 JRNL PMID 16838856 JRNL DOI 10.1080/15257770600686543 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY, REMARK 3 A.T. BRUNGER, H.M. BERMAN, NEW PARAMETERS FOR REMARK 3 THE REFINEMENT OF NUCLEIC ACID CONTAINING REMARK 3 STRUCTURES, ACTA CRYST. D52, 57-64 (1996). REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.6 REMARK 3 NUMBER OF REFLECTIONS : 458 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.294 REMARK 3 FREE R VALUE : 0.329 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 12.300 REMARK 3 FREE R VALUE TEST SET COUNT : 66 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 37 REMARK 3 BIN R VALUE (WORKING SET) : 0.3610 REMARK 3 BIN FREE R VALUE : 0.4690 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 7 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 334 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 300.0 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 : DNA_FREE.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : BRC_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : DNA_FREE.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : BRC.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FZA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000036490. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.900 REMARK 200 MONOCHROMATOR : ROTATED-INCLINED SI(111) DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE DIP-2040 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 525 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.605 REMARK 200 RESOLUTION RANGE LOW (A) : 31.496 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 14.50 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : 0.11200 REMARK 200 FOR THE DATA SET : 3.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.79 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 15.30 REMARK 200 R MERGE FOR SHELL (I) : 0.29300 REMARK 200 R SYM FOR SHELL (I) : 0.29300 REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM SODIUM CACODYLATE, 10MM SPERMINE REMARK 280 TETRAHYDROCHLORIDE, 20MM CALCIUM CHLORIDE, 100MM SODIUM CHLORIDE, REMARK 280 10%(V/V) 2-METHYL-2,4-PENTANEDIOL, PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 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 31.41300 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 31.41300 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.41300 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DNA HEXAPLEX GENERATE FROM THE REMARK 300 THREE DNA DUPLEX (X,Y,Z),(-Y,X-Y,Z) AND (-X+Y,-X,Z). 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: HEXAMERIC 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 18.18400 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 31.49561 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -18.18400 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 31.49561 REMARK 350 BIOMT3 3 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 CA CA A 11 LIES ON A SPECIAL POSITION. REMARK 375 NA NA A 13 LIES ON A SPECIAL POSITION. REMARK 375 NA NA A 15 LIES ON A SPECIAL POSITION. REMARK 375 CA CA B 12 LIES ON A SPECIAL POSITION. REMARK 375 NA NA B 14 LIES ON A SPECIAL POSITION. 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 NA A 15 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 5 O6 REMARK 620 2 DG B 5 O6 72.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 12 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 13 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 14 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 15 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 21 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 22 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UHX RELATED DB: PDB REMARK 900 ORIGINAL SEQUENCE CRYSTALLIZED UNDER CONDITION CONTAINING HEXAMMINE REMARK 900 COBALT CHLORIDE. REMARK 900 RELATED ID: 1V3P RELATED DB: PDB REMARK 900 ORIGINAL SEQUENCE CRYSTALLIZED UNDER LOWER POTASSIUM CONCENTRATION. REMARK 900 RELATED ID: 1V3O RELATED DB: PDB REMARK 900 ORIGINAL SEQUENCE CRYSTALLIZED UNDER HIGHER POTASSIUM CONCENTRATION. REMARK 900 RELATED ID: 1V3N RELATED DB: PDB REMARK 900 ORIGINAL SEQUENCE CRYSTALLIZED UNDER HIGHER POTASSIUM CONCENTRATION. REMARK 900 RELATED ID: 1UE3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE USED AS A MODEL IN AMORE. DBREF 2FZA A 1 8 PDB 2FZA 2FZA 1 8 DBREF 2FZA B 1 8 PDB 2FZA 2FZA 1 8 SEQRES 1 A 8 DG CBR DG DG DG DA DG DC SEQRES 1 B 8 DG CBR DG DG DG DA DG DC MODRES 2FZA CBR A 2 DC MODRES 2FZA CBR B 2 DC HET CBR A 2 20 HET CBR B 2 20 HET CA A 11 1 HET NA A 13 1 HET NA A 15 1 HET NA A 21 1 HET CA B 12 1 HET NA B 14 1 HET NA B 22 1 HETNAM CBR 5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION FORMUL 1 CBR 2(C9 H13 BR N3 O7 P) FORMUL 3 CA 2(CA 2+) FORMUL 4 NA 5(NA 1+) FORMUL 10 HOH *2(H2 O) LINK O3' DG A 1 P CBR A 2 1555 1555 1.61 LINK O3' CBR A 2 P DG A 3 1555 1555 1.60 LINK O3' DG B 1 P CBR B 2 1555 1555 1.61 LINK O3' CBR B 2 P DG B 3 1555 1555 1.61 LINK O6 DG A 5 NA NA A 15 1555 1555 2.83 LINK N7 DG A 7 NA NA A 21 1555 1555 2.88 LINK NA NA A 15 O6 DG B 5 1555 1555 2.80 LINK N7 DG B 7 NA NA B 22 1555 1555 2.88 SITE 1 AC1 1 DG B 3 SITE 1 AC2 1 DG A 4 SITE 1 AC3 1 DG B 4 SITE 1 AC4 2 DG A 5 DG B 5 SITE 1 AC5 1 DG A 7 SITE 1 AC6 1 DG B 7 CRYST1 36.368 36.368 62.826 90.00 90.00 120.00 P 63 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 0.027497 0.015875 0.000000 0.00000 SCALE2 0.000000 0.031750 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015917 0.00000