HEADER DEOXYRIBONUCLEIC ACID 03-JUN-99 475D OBSLTE 20-JUL-01 475D 1ENN TITLE WATER AND IONS IN A HIGH RESOLUTION STRUCTURE OF B-DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS B-DNA, BASE TRIPLET, IONS, ATOMIC RESOLUTION, KEYWDS 2 DEOXYRIBONUCLEIC ACID EXPDTA X-RAY DIFFRACTION AUTHOR M.SOLER-LOPEZ,L.MALININA,J.LIU,T.HUYNH-DINH,J.A.SUBIRANA REVDAT 3 20-JUL-01 475D 1 OBSLTE REVDAT 2 01-SEP-99 475D 1 JRNL REVDAT 1 14-JUN-99 475D 0 JRNL AUTH M.SOLER-LOPEZ,L.MALININA,J.LIU,T.HUYNH-DINH, JRNL AUTH 2 J.A.SUBIRANA JRNL TITL WATER AND IONS IN A HIGH RESOLUTION STRUCTURE OF JRNL TITL 2 B-DNA JRNL REF J.BIOL.CHEM. V. 274 23683 1999 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 0.89 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) : 0.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 CROSS-VALIDATION METHOD : R-FREE 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) : 0.155 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.145 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3201 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 32479 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.148 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.145 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.148 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2722 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 27733 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 381 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 144 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 506.89 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 10 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 5696 REMARK 3 NUMBER OF RESTRAINTS : 3872 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.041 REMARK 3 ANGLE DISTANCES (A) : 3.800 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) : 0.008 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.036 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER:J.MOL.BIOL.91,201- 228(1973). REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1.THERE ARE SEVERAL PHOSPHATES (2, REMARK 3 7, 11, 18) WHICH SHOULD BE MODELLED BY A CONTINUOUS REMARK 3 DISTRIBUTION OF DENSITY. AT PRESENT THEY ARE MODELLED AS A REMARK 3 DOUBLE CONFORMATION. AS A RESULT SOME OF THE STEREOCHEMICAL REMARK 3 PARAMETERS FOR THESE PHOSPHATES ARE NOT REASONABLE. WE EXPECT REMARK 3 TO IMPROVE THIS FEATURE OF THE MODEL. 2.THERE IS A STRING OF REMARK 3 RATHER CONTINUOUS ELECTRON DENSITY ON THE MAJOR GROOVE SIDE REMARK 3 WHICH HAS BEEN MODELLED AS WATER MOLECULES (NUMBERS 52, 53, REMARK 3 70, 89, 120, 149, 150,151, 155, 167, 168 AND 170 ) WHICH SHOW REMARK 3 MANY SHORT INTERMOLECULAR DISTANCES.SOME OF THEM MIGHT REMARK 3 CORRESPOND EITHER TO PARTIALLY ORDERED MG2+IONS OR TO REMARK 3 INADEQUATE MODELLING OF SOLVENT DISORDER. REMARK 4 REMARK 4 475D COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY THE NUCLEIC ACID DATABASE REMARK 100 ON 03-JUN-1999. REMARK 100 THE NDB ID CODE IS BD0016. REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*. REMARK 106 REMARK 106 THE HYDROGEN BONDS BETWEEN BASE PAIRS IN THIS ENTRY FOLLOW REMARK 106 THE CONVENTIONAL WATSON-CRICK HYDROGEN BONDING PATTERN. REMARK 106 THEY HAVE NOT BEEN PRESENTED ON *CONECT* RECORDS IN THIS REMARK 106 ENTRY. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-1998 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9076 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32684 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.890 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 (%) : 97.6 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.05900 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) : 0.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.43 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 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 (%): 33.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.00 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 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-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 10.96600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.36650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.25950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.36650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 10.96600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.25950 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O HOH 149 O HOH 155 1.67 REMARK 500 O HOH 52 O HOH 170 1.95 REMARK 500 O HOH 52 O HOH 53 1.97 REMARK 500 O HOH 52 O HOH 168 2.01 REMARK 500 O HOH 89 O HOH 155 2.02 REMARK 500 O HOH 149 O HOH 155 2.02 REMARK 500 O HOH 70 O HOH 151 2.05 REMARK 500 O HOH 52 O HOH 120 2.17 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 143 DISTANCE = 7.74 ANGSTROMS REMARK 525 HOH 152 DISTANCE = 7.24 ANGSTROMS SEQRES 1 A 9 G C G A A T T C G SEQRES 1 B 9 G C G A A T T C G HET MG 19 1 HET MG 26 1 HET MG 31 1 HET MG 38 1 HET MG 44 1 HET CL 301 1 HET NA 201 1 HET NA 202 1 HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION FORMUL 3 MG 5(MG 2+) FORMUL 8 CL CL 1- FORMUL 9 NA 2(NA 1+) FORMUL 11 HOH *139(H2 O1) CRYST1 21.932 36.519 52.733 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 0.045595 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027383 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018963 0.00000