HEADER DNA 18-APR-01 1IH3 TITLE MULTI-CONFORMATION CRYSTAL STRUCTURE OF GGM5CGM5CC COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS B TO A DNA TRANSITION, DNA TRANSITION, STRUCTURAL TRANSITION, DNA EXPDTA X-RAY DIFFRACTION AUTHOR J.M.VARGASON,K.HENDERSON,P.S.HO REVDAT 4 07-FEB-24 1IH3 1 LINK REVDAT 3 04-OCT-17 1IH3 1 REMARK REVDAT 2 24-FEB-09 1IH3 1 VERSN REVDAT 1 18-JUN-01 1IH3 0 JRNL AUTH J.M.VARGASON,K.HENDERSON,P.S.HO JRNL TITL A CRYSTALLOGRAPHIC MAP OF THE TRANSITION FROM B-DNA TO JRNL TITL 2 A-DNA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 98 7265 2001 JRNL REFN ISSN 0027-8424 JRNL PMID 11390969 JRNL DOI 10.1073/PNAS.121176898 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 7269 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) : 0.173 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 325 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 976 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.70 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) : 0.003 REMARK 3 BOND ANGLES (DEGREES) : 0.820 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 : 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 1IH3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013259. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-SEP-99 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 6.0 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7273 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.35300 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM CHLORIDE, SODIUM CACODYLATE, REMARK 280 SPERMINE TETRAHYDROCHLORIDE, PH 6.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 119.59933 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 59.79967 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 59.79967 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 119.59933 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IH1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC RESOLVED TO 2.0 REMARK 900 ANGSTROM RESOLUTION REMARK 900 RELATED ID: 1IH2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GGBR5CGBR5CC REMARK 900 RELATED ID: 1IH4 RELATED DB: PDB REMARK 900 MULTI-CONFORMATION CRYSTAL STRUCTURE OF GGM5CGCC REMARK 900 RELATED ID: 1IH6 RELATED DB: PDB REMARK 900 MULTI-CONFORMATION CRYSTAL STRUCTURE OF GGBR5CGCC DBREF 1IH3 A 1 6 PDB 1IH3 1IH3 1 6 DBREF 1IH3 B 7 12 PDB 1IH3 1IH3 7 12 DBREF 1IH3 C 13 18 PDB 1IH3 1IH3 13 18 DBREF 1IH3 D 19 24 PDB 1IH3 1IH3 19 24 DBREF 1IH3 E 25 30 PDB 1IH3 1IH3 25 30 DBREF 1IH3 F 31 36 PDB 1IH3 1IH3 31 36 DBREF 1IH3 G 37 42 PDB 1IH3 1IH3 37 42 DBREF 1IH3 H 43 48 PDB 1IH3 1IH3 43 48 SEQRES 1 A 6 DG DG 5CM DG 5CM DC SEQRES 1 B 6 DG DG 5CM DG 5CM DC SEQRES 1 C 6 DG DG 5CM DG 5CM DC SEQRES 1 D 6 DG DG 5CM DG 5CM DC SEQRES 1 E 6 DG DG 5CM DG 5CM DC SEQRES 1 F 6 DG DG 5CM DG 5CM DC SEQRES 1 G 6 DG DG 5CM DG 5CM DC SEQRES 1 H 6 DG DG 5CM DG 5CM DC MODRES 1IH3 5CM A 3 DC MODRES 1IH3 5CM A 5 DC MODRES 1IH3 5CM B 9 DC MODRES 1IH3 5CM B 11 DC MODRES 1IH3 5CM C 15 DC MODRES 1IH3 5CM C 17 DC MODRES 1IH3 5CM D 21 DC MODRES 1IH3 5CM D 23 DC MODRES 1IH3 5CM E 27 DC MODRES 1IH3 5CM E 29 DC MODRES 1IH3 5CM F 33 DC MODRES 1IH3 5CM F 35 DC MODRES 1IH3 5CM G 39 DC MODRES 1IH3 5CM G 41 DC MODRES 1IH3 5CM H 45 DC MODRES 1IH3 5CM H 47 DC HET 5CM A 3 20 HET 5CM A 5 20 HET 5CM B 9 20 HET 5CM B 11 20 HET 5CM C 15 20 HET 5CM C 17 20 HET 5CM D 21 20 HET 5CM D 23 20 HET 5CM E 27 20 HET 5CM E 29 20 HET 5CM F 33 20 HET 5CM F 35 20 HET 5CM G 39 20 HET 5CM G 41 20 HET 5CM H 45 20 HET 5CM H 47 20 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 5CM 16(C10 H16 N3 O7 P) FORMUL 9 HOH *73(H2 O) LINK O3' DG A 2 P 5CM A 3 1555 1555 1.61 LINK O3' 5CM A 3 P DG A 4 1555 1555 1.61 LINK O3' DG A 4 P 5CM A 5 1555 1555 1.61 LINK O3' 5CM A 5 P DC A 6 1555 1555 1.60 LINK O3' DG B 8 P 5CM B 9 1555 1555 1.61 LINK O3' 5CM B 9 P DG B 10 1555 1555 1.61 LINK O3' DG B 10 P 5CM B 11 1555 1555 1.61 LINK O3' 5CM B 11 P DC B 12 1555 1555 1.60 LINK O3' DG C 14 P 5CM C 15 1555 1555 1.60 LINK O3' 5CM C 15 P DG C 16 1555 1555 1.61 LINK O3' DG C 16 P 5CM C 17 1555 1555 1.61 LINK O3' 5CM C 17 P DC C 18 1555 1555 1.61 LINK O3' DG D 20 P 5CM D 21 1555 1555 1.61 LINK O3' 5CM D 21 P DG D 22 1555 1555 1.60 LINK O3' DG D 22 P 5CM D 23 1555 1555 1.61 LINK O3' 5CM D 23 P DC D 24 1555 1555 1.61 LINK O3' DG E 26 P 5CM E 27 1555 1555 1.60 LINK O3' 5CM E 27 P DG E 28 1555 1555 1.60 LINK O3' DG E 28 P 5CM E 29 1555 1555 1.60 LINK O3' 5CM E 29 P DC E 30 1555 1555 1.61 LINK O3' DG F 32 P 5CM F 33 1555 1555 1.60 LINK O3' 5CM F 33 P DG F 34 1555 1555 1.61 LINK O3' DG F 34 P 5CM F 35 1555 1555 1.61 LINK O3' 5CM F 35 P DC F 36 1555 1555 1.60 LINK O3' DG G 38 P 5CM G 39 1555 1555 1.60 LINK O3' 5CM G 39 P DG G 40 1555 1555 1.61 LINK O3' DG G 40 P 5CM G 41 1555 1555 1.61 LINK O3' 5CM G 41 P DC G 42 1555 1555 1.61 LINK O3' DG H 44 P 5CM H 45 1555 1555 1.61 LINK O3' 5CM H 45 P DG H 46 1555 1555 1.61 LINK O3' DG H 46 P 5CM H 47 1555 1555 1.61 LINK O3' 5CM H 47 P DC H 48 1555 1555 1.61 CRYST1 42.345 42.345 179.399 90.00 90.00 120.00 P 32 2 1 48 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 0.023616 0.013634 0.000000 0.00000 SCALE2 0.000000 0.027269 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005574 0.00000