PDB Short entry for 1YBC HEADER DNA 20-DEC-04 1YBC TITLE CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2-(BENZYLOXY) TITLE 2 ETHYL] THYMIDINE (T*) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*TP*AP*(BOE)P*AP*CP*GP*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS A-DNA, O2'-MODIFICATION, DECAMER, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.EGLI,G.MINASOV,V.TERESHKO,P.S.PALLAN,M.TEPLOVA,G.B.INAMATI, AUTHOR 2 E.A.LESNIK,S.R.OWENS,B.S.ROSS,T.P.PRAKASH,M.MANOHARAN REVDAT 3 23-AUG-23 1YBC 1 REMARK LINK REVDAT 2 24-FEB-09 1YBC 1 VERSN REVDAT 1 28-JUN-05 1YBC 0 JRNL AUTH M.EGLI,G.MINASOV,V.TERESHKO,P.S.PALLAN,M.TEPLOVA, JRNL AUTH 2 G.B.INAMATI,E.A.LESNIK,S.R.OWENS,B.S.ROSS,T.P.PRAKASH, JRNL AUTH 3 M.MANOHARAN JRNL TITL PROBING THE INFLUENCE OF STEREOELECTRONIC EFFECTS ON THE JRNL TITL 2 BIOPHYSICAL PROPERTIES OF OLIGONUCLEOTIDES: COMPREHENSIVE JRNL TITL 3 ANALYSIS OF THE RNA AFFINITY, NUCLEASE RESISTANCE, AND JRNL TITL 4 CRYSTAL STRUCTURE OF TEN 2'-O-RIBONUCLEIC ACID JRNL TITL 5 MODIFICATIONS. JRNL REF BIOCHEMISTRY V. 44 9045 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15966728 JRNL DOI 10.1021/BI050574M REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 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) (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 4851 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) : 0.170 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 532 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2281 REMARK 3 BIN FREE R VALUE : 0.2634 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 38 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 : 426 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 98 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.33600 REMARK 3 B22 (A**2) : 2.13400 REMARK 3 B33 (A**2) : -1.79700 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) : 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.280 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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: CONJUGATE GRADIENT REFINEMENT USING REMARK 3 MAXIMUM LIKELIHOOD TARGET FOR AMPLITUDES REMARK 4 REMARK 4 1YBC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031338. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-DEC-98 REMARK 200 TEMPERATURE (KELVIN) : 110 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5065 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.34800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.34800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 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: PDB ENTRY 410D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10%MPD, 40MM NA-CACODILATE, 12 MM REMARK 280 SPERMINE, 80MM SRCL2, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 12.53150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.72900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.18250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.72900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.53150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.18250 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 300 REMARK: CHAINS A AND B FORM DUPLEX 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 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 DG B 19 0.06 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 SR A 100 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 O6 REMARK 620 2 HOH A 101 O 73.0 REMARK 620 3 HOH A 104 O 97.5 120.1 REMARK 620 4 HOH A 105 O 75.3 146.7 73.7 REMARK 620 5 HOH B 102 O 131.7 112.9 115.9 81.6 REMARK 620 6 HOH B 103 O 152.7 88.2 74.7 125.1 73.5 REMARK 620 7 HOH B 106 O 84.4 68.1 171.8 99.2 58.1 107.1 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR A 100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y7F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2- REMARK 900 [HYDROXY(METHYLENEAMINO)OXY]ETHYL] THYMIDINE (T*) REMARK 900 RELATED ID: 1Y84 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2- REMARK 900 (IMIDAZOLYL)ETHYL] THYMIDINE (T*) REMARK 900 RELATED ID: 1Y86 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2-(FLUORO) REMARK 900 ETHYL] THYMIDINE (T*) REMARK 900 RELATED ID: 1Y8L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2-(TRIFLUORO) REMARK 900 ETHYL] THYMIDINE (T*) REMARK 900 RELATED ID: 1Y8V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-PROPYL REMARK 900 THYMIDINE (T*) REMARK 900 RELATED ID: 1Y9S RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-PROPARGYL REMARK 900 THYMIDINE (T*) REMARK 900 RELATED ID: 1WV5 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O- REMARK 900 BUTYL THYMINE IN PLACE OF T6, MG-FORM REMARK 900 RELATED ID: 1WV6 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O- REMARK 900 BUTYL THYMINE IN PLACE OF T6, SR-FORM REMARK 900 RELATED ID: 1Y9F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-ALLYL REMARK 900 THYMIDINE (T*) REMARK 900 RELATED ID: 1YB9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2-(N,N- REMARK 900 DIMETHYLAMINOOXY)ETHYL] THYMIDINE (T*) DBREF 1YBC A 1 10 PDB 1YBC 1YBC 1 10 DBREF 1YBC B 11 20 PDB 1YBC 1YBC 11 20 SEQRES 1 A 10 DG DC DG DT DA BOE DA DC DG DC SEQRES 1 B 10 DG DC DG DT DA BOE DA DC DG DC MODRES 1YBC BOE A 6 DT MODRES 1YBC BOE B 16 DT HET BOE A 6 31 HET BOE B 16 31 HET SR A 100 1 HETNAM BOE 2'-O-[2-(BENZYLOXY)ETHYL] THYMIDINE-5'-MONOPHOSPHATE HETNAM SR STRONTIUM ION FORMUL 1 BOE 2(C19 H25 N2 O10 P) FORMUL 3 SR SR 2+ FORMUL 4 HOH *98(H2 O) LINK O3' DA A 5 P BOE A 6 1555 1555 1.60 LINK O3' BOE A 6 P DA A 7 1555 1555 1.59 LINK O3' DA B 15 P BOE B 16 1555 1555 1.61 LINK O3' BOE B 16 P DA B 17 1555 1555 1.59 LINK O6 DG A 3 SR SR A 100 1555 1555 2.69 LINK SR SR A 100 O HOH A 101 1555 1555 2.45 LINK SR SR A 100 O HOH A 104 1555 1555 2.69 LINK SR SR A 100 O HOH A 105 1555 1555 2.54 LINK SR SR A 100 O HOH B 102 1555 1555 2.61 LINK SR SR A 100 O HOH B 103 1555 1555 2.86 LINK SR SR A 100 O HOH B 106 1555 1555 2.62 SITE 1 AC1 7 DG A 3 HOH A 101 HOH A 104 HOH A 105 SITE 2 AC1 7 HOH B 102 HOH B 103 HOH B 106 CRYST1 25.063 44.365 45.458 90.00 90.00 90.00 P 21 21 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 0.039899 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021998 0.00000