PDB Short entry for 1D9R HEADER DNA 29-OCT-99 1D9R TITLE CRYSTAL STRUCTURE OF DNA SHEARED TANDEM G-A BASE PAIRS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*GP*AP*AP*(BRU)P*GP*AP*GP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS TANDEM GA BASE PAIRS, GA MISMATCH, DEOXYRIBONUCLEIC ACID, DNA EXPDTA X-RAY DIFFRACTION AUTHOR Y.-G.GAO,H.ROBINSON,R.SANISHVILI,A.JOACHIMIAK,A.H.-J.WANG REVDAT 6 24-JUL-19 1D9R 1 REMARK LINK REVDAT 5 24-FEB-09 1D9R 1 VERSN REVDAT 4 01-APR-03 1D9R 1 JRNL REVDAT 3 26-SEP-01 1D9R 3 ATOM REVDAT 2 01-JAN-00 1D9R 1 JRNL REVDAT 1 05-NOV-99 1D9R 0 JRNL AUTH Y.G.GAO,H.ROBINSON,R.SANISHVILI,A.JOACHIMIAK,A.H.WANG JRNL TITL STRUCTURE AND RECOGNITION OF SHEARED TANDEM G X A BASE PAIRS JRNL TITL 2 ASSOCIATED WITH HUMAN CENTROMERE DNA SEQUENCE AT ATOMIC JRNL TITL 3 RESOLUTION. JRNL REF BIOCHEMISTRY V. 38 16452 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10600106 JRNL DOI 10.1021/BI9914614 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 CROSS-VALIDATION METHOD : A POSTERIORI REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.234 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.234 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 437 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 8923 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 412 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2220 REMARK 3 NUMBER OF RESTRAINTS : 1837 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.052 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.003 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.072 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: SHELXL SWAT OPTION REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : G.PARKINSON, J.VOJTECHOVSKY, REMARK 3 L.CLOWNEY, A.T.BRUNGER, H.M.BERMAN REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SHELXL HOPE OPTION REMARK 4 REMARK 4 1D9R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-99. REMARK 100 THE DEPOSITION ID IS D_1000009921. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-98 REMARK 200 TEMPERATURE (KELVIN) : 123 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9611 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8923 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 0.37700 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: MAD PHASING BY BROMINES REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, COBALT HEXAMMINE, MGCL2, TRIS, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 36.25200 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 36.25200 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 11.35550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.60800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 11.35550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.60800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 36.25200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 11.35550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.60800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 36.25200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 11.35550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 33.60800 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: 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 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 CO NCO A 21 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1117 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC A 2 N1 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = -7.3 DEGREES REMARK 500 DC B 12 C5 - C4 - N4 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA B 15 O4' - C1' - N9 ANGL. DEV. = -7.2 DEGREES REMARK 500 DA B 15 C6 - N1 - C2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA B 15 C5 - C6 - N1 ANGL. DEV. = -3.5 DEGREES REMARK 500 DA B 15 N1 - C6 - N6 ANGL. DEV. = 4.9 DEGREES REMARK 500 DG B 17 C6 - N1 - C2 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG B 17 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA B 18 C2 - N3 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG B 19 C2 - N3 - C4 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 19 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG B 20 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG B 20 O4' - C1' - N9 ANGL. DEV. = -7.5 DEGREES 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 NCO A 21 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NCO A 21 N2 REMARK 620 2 NCO A 21 N1 88.0 REMARK 620 3 NCO A 21 N2 175.6 88.9 REMARK 620 4 NCO A 21 N3 92.3 89.5 90.8 REMARK 620 5 NCO A 21 N4 88.8 90.2 88.0 178.8 REMARK 620 6 NCO A 21 N5 0.0 88.0 175.6 92.3 88.8 REMARK 620 7 NCO A 21 N6 90.8 178.7 92.3 91.0 89.4 90.7 REMARK 620 8 NCO A 21 N4 88.0 0.0 88.8 89.5 90.2 88.1 178.7 REMARK 620 9 NCO A 21 N5 175.6 88.9 0.0 90.8 88.1 175.6 92.4 88.8 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 21 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: BD0024 RELATED DB: NDB REMARK 900 CRYSTAL STRUCTURE OF DNA SHEARED TANDEM G A BASE PAIRS DBREF 1D9R A 1 10 PDB 1D9R 1D9R 1 10 DBREF 1D9R B 11 20 PDB 1D9R 1D9R 11 20 SEQRES 1 A 10 DC DC DG DA DA BRU DG DA DG DG SEQRES 1 B 10 DC DC DG DA DA BRU DG DA DG DG MODRES 1D9R BRU A 6 DU MODRES 1D9R BRU B 16 DU HET BRU A 6 20 HET BRU B 16 20 HET NCO A 21 7 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM NCO COBALT HEXAMMINE(III) FORMUL 1 BRU 2(C9 H12 BR N2 O8 P) FORMUL 3 NCO CO H18 N6 3+ FORMUL 4 HOH *133(H2 O) LINK CO NCO A 21 N2 NCO A 21 1555 3555 1.99 LINK CO NCO A 21 N4 NCO A 21 1555 3555 2.02 LINK CO NCO A 21 N5 NCO A 21 1555 3555 1.99 LINK CO NCO A 21 N1 NCO A 21 1555 3555 2.02 LINK CO NCO A 21 N6 NCO A 21 1555 3555 2.01 LINK CO NCO A 21 N3 NCO A 21 1555 3555 2.01 LINK O3' DA A 5 P BRU A 6 1555 1555 1.64 LINK O3' BRU A 6 P DG A 7 1555 1555 1.61 LINK O3' DA B 15 P BRU B 16 1555 1555 1.60 LINK O3' BRU B 16 P DG B 17 1555 1555 1.59 SITE 1 AC1 5 DC A 2 DG A 3 HOH A1056 HOH A1069 SITE 2 AC1 5 DG B 17 CRYST1 22.711 67.216 72.504 90.00 90.00 90.00 C 2 2 21 16 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 0.044032 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014877 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013792 0.00000