PDB Short entry for 1D8X HEADER DNA 26-OCT-99 1D8X 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*TP*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, DNA EXPDTA X-RAY DIFFRACTION AUTHOR Y.-G.GAO,H.ROBINSON,R.SANISHVILI,A.JOACHIMIAK,A.H.-J.WANG REVDAT 7 07-FEB-24 1D8X 1 REMARK LINK REVDAT 6 04-OCT-17 1D8X 1 REMARK REVDAT 5 24-FEB-09 1D8X 1 VERSN REVDAT 4 01-APR-03 1D8X 1 JRNL REVDAT 3 01-JAN-00 1D8X 1 JRNL REVDAT 2 26-NOV-99 1D8X 1 REMARK REVDAT 1 05-NOV-99 1D8X 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. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.7 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) : 0.188 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.188 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 633 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 12550 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.182 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.182 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 566 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 11236 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 : 9 REMARK 3 SOLVENT ATOMS : 138 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 : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4386 REMARK 3 NUMBER OF RESTRAINTS : 5330 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.073 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.007 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.044 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: NULL REMARK 4 REMARK 4 1D8X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1000009901. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-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) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 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 IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : D*TREK V. 5.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12550 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 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 (%) : 81.7 REMARK 200 DATA REDUNDANCY : 1.600 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 46.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.25 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, COBALT HEXAMMINE, MGCL2, TRIS, PH REMARK 280 7.5, VAPOR DIFFUSION, TEMPERATURE 298K 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 31.39200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.84250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 31.39200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.84250 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: 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 HOH A 100 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 101 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 211 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 219 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 1 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC A 1 N3 - C4 - C5 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG A 3 C6 - C5 - N7 ANGL. DEV. = -4.2 DEGREES REMARK 500 DA A 4 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 DA A 4 N9 - C4 - C5 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA A 5 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG A 7 O5' - P - OP2 ANGL. DEV. = -6.0 DEGREES REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG A 7 C6 - N1 - C2 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG A 7 N1 - C2 - N3 ANGL. DEV. = 4.2 DEGREES REMARK 500 DC B 11 N3 - C4 - C5 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 11 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 DC B 11 C3' - O3' - P ANGL. DEV. = -9.4 DEGREES REMARK 500 DA B 14 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA B 15 O4' - C4' - C3' ANGL. DEV. = -3.3 DEGREES 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 DA A 5 0.08 SIDE CHAIN REMARK 500 DC B 11 0.08 SIDE CHAIN REMARK 500 DA B 14 0.08 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 MG A 22 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA A 5 OP2 REMARK 620 2 HOH A 228 O 86.3 REMARK 620 3 HOH A 229 O 95.1 178.0 REMARK 620 4 HOH A 230 O 88.8 89.9 88.7 REMARK 620 5 HOH A 231 O 173.0 88.7 89.8 86.3 REMARK 620 6 HOH A 232 O 95.6 91.5 89.8 175.5 89.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 23 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 9 OP1 REMARK 620 2 HOH A 233 O 87.6 REMARK 620 3 HOH A 234 O 89.6 173.2 REMARK 620 4 HOH A 235 O 89.9 95.6 90.6 REMARK 620 5 HOH A 236 O 175.6 93.4 89.9 85.8 REMARK 620 6 HOH A 237 O 97.8 85.1 89.2 172.4 86.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 22 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 23 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 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: BD0025 RELATED DB: NDB REMARK 900 CRYSTAL STRUCTURE OF DNA SHEARED TANDEM G-A BASE PAIRS DBREF 1D8X A 1 10 PDB 1D8X 1D8X 1 10 DBREF 1D8X B 11 20 PDB 1D8X 1D8X 11 20 SEQRES 1 A 10 DC DC DG DA DA DT DG DA DG DG SEQRES 1 B 10 DC DC DG DA DA DT DG DA DG DG HET MG A 22 1 HET MG A 23 1 HET NCO A 21 7 HETNAM MG MAGNESIUM ION HETNAM NCO COBALT HEXAMMINE(III) FORMUL 3 MG 2(MG 2+) FORMUL 5 NCO CO H18 N6 3+ FORMUL 6 HOH *138(H2 O) LINK OP2 DA A 5 MG MG A 22 1555 1555 1.97 LINK OP1 DG A 9 MG MG A 23 1555 1555 2.08 LINK MG MG A 22 O HOH A 228 1555 1555 2.07 LINK MG MG A 22 O HOH A 229 1555 1555 2.04 LINK MG MG A 22 O HOH A 230 1555 1555 2.07 LINK MG MG A 22 O HOH A 231 1555 1555 2.07 LINK MG MG A 22 O HOH A 232 1555 1555 2.05 LINK MG MG A 23 O HOH A 233 1555 1555 2.03 LINK MG MG A 23 O HOH A 234 1555 1555 2.06 LINK MG MG A 23 O HOH A 235 1555 1555 2.04 LINK MG MG A 23 O HOH A 236 1555 1555 2.09 LINK MG MG A 23 O HOH A 237 1555 1555 2.08 SITE 1 AC1 6 DA A 5 HOH A 228 HOH A 229 HOH A 230 SITE 2 AC1 6 HOH A 231 HOH A 232 SITE 1 AC2 6 DG A 9 HOH A 233 HOH A 234 HOH A 235 SITE 2 AC2 6 HOH A 236 HOH A 237 SITE 1 AC3 9 DG A 3 DT A 6 DG A 7 HOH A 167 SITE 2 AC3 9 HOH A 170 HOH A 209 DG B 13 DG B 17 SITE 3 AC3 9 HOH B 125 CRYST1 62.784 35.685 22.466 90.00 104.38 90.00 C 1 2 1 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 0.015928 0.000000 0.004084 0.00000 SCALE2 0.000000 0.028023 0.000000 0.00000 SCALE3 0.000000 0.000000 0.045951 0.00000