10 20 30 40 50 60 70 80 461D - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 12-MAR-99 461D
TITLE A "HYDRAT-ION SPINE" IN A B-DNA MINOR GROOVE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(TAF) COMPND 3 P*TP*CP*GP*CP*G)-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS B-DNA, DODECAMER DUPLEX, TYPE 2 RB+ FORM CRYSTAL
EXPDTA X-RAY DIFFRACTION
AUTHOR V.TERESHKO,G.MINASOV,M.EGLI
REVDAT 2 24-FEB-09 461D 1 VERSN REVDAT 1 08-APR-99 461D 0
JRNL AUTH V.TERESHKO,G.MINASOV,M.EGLI JRNL TITL A "HYDRAT-ION SPINE" IN A B-DNA MINOR GROOVE JRNL REF J.AM.CHEM.SOC. V. 121 3590 1999 JRNL REFN ISSN 0002-7863
REMARK 1
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) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.186 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.186 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 10813 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 : 508 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 160 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 : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 ANGLE DISTANCES (A) : 0.017 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 461D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 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 : 10813 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.09400 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: NULL 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 (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SITTING DROPLETS CONTAINING 1.2 MM REMARK 280 OLIGONUCLEOTIDE, 20 MM RB CACODYLATE PH 6.9, 6.2 MM MAGNESIUM REMARK 280 ACETATE, 3.2 MM SPERMINE TETRACHLORIDE AGAINST RESERVOIR OF REMARK 280 40% MPD, VAPOR DIFFUSION, SITTING DROP, 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 12.53500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.88500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.86000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.88500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.53500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.86000 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 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 9 O4' - C1' - N1 ANGL. DEV. = -5.9 DEGREES REMARK 500 DG A 10 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 265
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 25 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 26 O REMARK 620 2 HOH B 30 O 95.7 REMARK 620 3 HOH A 28 O 93.1 86.7 REMARK 620 4 HOH B 31 O 87.8 175.9 95.3 REMARK 620 5 HOH B 27 O 175.1 89.3 86.7 87.3 REMARK 620 6 HOH B 29 O 87.3 88.9 175.6 89.1 93.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 RB A 110 RB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 8 O4' REMARK 620 2 HOH A 265 O 75.7 REMARK 620 3 HOH A 131 O 76.5 69.0 REMARK 620 4 DT B 20 O4' 159.5 83.9 98.0 REMARK 620 5 HOH B 145 O 94.6 69.7 138.6 76.4 REMARK 620 6 TAF A 7 O2 64.7 137.1 114.2 133.9 97.0 REMARK 620 7 TAF B 19 O2 133.8 143.8 95.0 65.8 118.1 78.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 32 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 34 O REMARK 620 2 HOH B 37 O 74.4 REMARK 620 3 HOH A 36 O 85.3 86.5 REMARK 620 4 HOH A2001 O 95.8 161.7 77.2 REMARK 620 5 HOH B 33 O 74.4 76.6 156.4 116.2 REMARK 620 6 HOH A 35 O 100.8 166.4 80.3 5.6 114.9 REMARK 620 7 TAF B 19 OP1 164.4 92.3 85.8 94.6 111.0 90.2 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 RB A 110 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 25 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 32
DBREF 461D A 1 12 PDB 461D 461D 1 12 DBREF 461D B 13 24 PDB 461D 461D 13 24
SEQRES 1 A 12 DC DG DC DG DA DA TAF DT DC DG DC DG SEQRES 1 B 12 DC DG DC DG DA DA TAF DT DC DG DC DG
MODRES 461D TAF A 7 DT MODRES 461D TAF B 19 DT
HET TAF A 7 21 HET TAF B 19 21 HET RB A 110 1 HET MG A 25 1 HET MG B 32 1
HETNAM TAF 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE-5'- HETNAM 2 TAF PHOSPHATE HETNAM RB RUBIDIUM ION HETNAM MG MAGNESIUM ION
FORMUL 1 TAF 2(C10 H14 F N2 O8 P) FORMUL 3 RB RB 1+ FORMUL 4 MG 2(MG 2+) FORMUL 6 HOH *160(H2 O)
LINK O3' DA A 6 P TAF A 7 1555 1555 1.60 LINK O3' TAF A 7 P DT A 8 1555 1555 1.61 LINK MG MG A 25 O HOH A 26 1555 1555 2.21 LINK MG MG A 25 O HOH B 30 1555 1555 2.14 LINK MG MG A 25 O HOH A 28 1555 1555 2.08 LINK MG MG A 25 O HOH B 31 1555 1555 2.14 LINK MG MG A 25 O HOH B 27 1555 1555 2.12 LINK MG MG A 25 O HOH B 29 1555 1555 2.13 LINK RB RB A 110 O4' DT A 8 1555 1555 3.47 LINK RB RB A 110 O HOH A 265 1555 1555 3.21 LINK RB RB A 110 O HOH A 131 1555 1555 2.80 LINK RB RB A 110 O4' DT B 20 1555 1555 3.31 LINK RB RB A 110 O HOH B 145 1555 1555 2.77 LINK RB RB A 110 O2 TAF A 7 1555 1555 2.82 LINK RB RB A 110 O2 TAF B 19 1555 1555 2.71 LINK O3' DA B 18 P TAF B 19 1555 1555 1.60 LINK O3' TAF B 19 P DT B 20 1555 1555 1.61 LINK MG MG B 32 O HOH B 34 1555 1555 2.18 LINK MG MG B 32 O HOH B 37 1555 1555 2.05 LINK MG MG B 32 O HOH A 36 1555 2554 2.12 LINK MG MG B 32 O HOH A2001 1555 2554 1.89 LINK MG MG B 32 O HOH B 33 1555 3645 2.06 LINK MG MG B 32 O HOH A 35 1555 2554 1.99 LINK MG MG B 32 OP1 TAF B 19 1555 3645 2.18
SITE 1 AC1 6 TAF A 7 DT A 8 HOH A 131 TAF B 19 SITE 2 AC1 6 DT B 20 HOH B 145 SITE 1 AC2 6 HOH A 26 HOH A 28 HOH B 27 HOH B 29 SITE 2 AC2 6 HOH B 30 HOH B 31 SITE 1 AC3 7 HOH A 35 HOH A 36 HOH A2001 TAF B 19 SITE 2 AC3 7 HOH B 33 HOH B 34 HOH B 37
CRYST1 25.070 39.720 65.770 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 0.039888 0.000000 0.000000 0.00000
SCALE2 0.000000 0.025176 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015205 0.00000