HEADER DNA 20-APR-07 2PLO TITLE D-(GTATACC) LOW TEMPERATURE (100K) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*DGP*DGP*DTP*DAP*DTP*DAP*DCP*DC)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: AUTOMATED SOLID SYNTHESIS KEYWDS DNA, HIGH PRESSURE, LOW TEMPERATURE, COMPRESSIBILITY, KEYWDS 2 CRYSTALS EXPDTA X-RAY DIFFRACTION AUTHOR T.PRANGE,M.LECOUVEY,E.MIGIANU-GRIFFONI REVDAT 2 24-FEB-09 2PLO 1 VERSN REVDAT 1 27-MAY-08 2PLO 0 JRNL AUTH T.PRANGE,E.GIRARD,R.KAHN,M.LECOUVEY, JRNL AUTH 2 E.MIGIANU-GRIFFONI,M.MEZOUAR,R.FOURME JRNL TITL ADAPTATION OF MACROMOLECULAR CRYSTALS TO EXTREME JRNL TITL 2 CONDITIONS: HIGH PRESSURE VERSUS LOW TEMPERATURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.GIRARD,T.PRANGE,A.C.DHAUSSY,E.MIGIANU-GRIFFONI, REMARK 1 AUTH 2 M.LECOUVEY,J.C.CHERVIN,M.MEZOUAR,R.KAHN,R.FOURME REMARK 1 TITL ADAPTATION OF BASE PAIRED DOUBLE HELIX REMARK 1 TITL 2 ARCHITECTURE TO EXTREME PRESSURE REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 CROSS-VALIDATION METHOD : NONE 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) : 0.180 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.177 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) : 9357 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.177 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)) : 8870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 322 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 70 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 393.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 182.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1579 REMARK 3 NUMBER OF RESTRAINTS : 1606 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.098 REMARK 3 ANGLE DISTANCES (A) : 0.295 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.001 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.015 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.026 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.027 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 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 2PLO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-APR-07. REMARK 100 THE RCSB ID CODE IS RCSB042513. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.962 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : SI(111) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9382 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.19100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 2PL8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MG DISSOLVED IN 0.2 ML OF 15 % REMARK 280 MPD, 10-2 M SODIUM CACODYLATE BUFFER. ADDITIVES : 10-5M SODIUM REMARK 280 AZIDE, 10-2 M MGCL2 AND 2.10-2 M SPERMINE CHLORIDE, PH 7, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 13.79767 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.59533 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 20.69650 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 34.49417 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 6.89883 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: A FORM OF DNA - DOUBLE STRANDED HELIX 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.7 KCAL/MOL 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 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.0 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 NA A 20 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 24 O REMARK 620 2 HOH A 21 O 89.5 REMARK 620 3 HOH A 22 O 172.6 90.0 REMARK 620 4 HOH A 25 O 93.8 93.9 93.6 REMARK 620 5 HOH A 23 O 89.5 172.2 89.9 93.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 20 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 115D RELATED DB: PDB REMARK 900 D-(GG[BR]UA[BR]UACC), WITH THE TWO BR REPLACING THY METHYL REMARK 900 GROUPS REMARK 900 RELATED ID: 1VJ4 RELATED DB: PDB REMARK 900 D-(GGTATACC) INITIAL STRUCTURE REMARK 900 RELATED ID: 2PKV RELATED DB: PDB REMARK 900 D-(GGTATACC) AMBIENT PRESSURE REMARK 900 RELATED ID: 2PL4 RELATED DB: PDB REMARK 900 D-(GGTATACC) UNDER 0.55 GPA HYDROSTATIC PRESSURE REMARK 900 RELATED ID: 2PL8 RELATED DB: PDB REMARK 900 D-(GGTATACC) UNDER 1.04 GPA HYDROSTATIC PRESSURE REMARK 900 RELATED ID: 2PLB RELATED DB: PDB REMARK 900 D-(GGTATACC) AT 1.39 GPA HYDROSTATIC PRESSURE REMARK 900 RELATED ID: 2PLO RELATED DB: PDB REMARK 900 D-(GTATACC) LOW TEMPERATURE (100K) DBREF 2PLO A 1 8 PDB 2PLO 2PLO 1 8 DBREF 2PLO B 1 8 PDB 2PLO 2PLO 1 8 SEQRES 1 A 8 DG DG DT DA DT DA DC DC SEQRES 1 B 8 DG DG DT DA DT DA DC DC HET NA A 20 1 HETNAM NA SODIUM ION FORMUL 3 NA NA 1+ FORMUL 4 HOH *70(H2 O) LINK NA NA A 20 O HOH A 24 1555 1555 2.07 LINK NA NA A 20 O HOH A 21 1555 1555 2.06 LINK NA NA A 20 O HOH A 22 1555 1555 2.07 LINK NA NA A 20 O HOH A 25 1555 1555 2.05 LINK NA NA A 20 O HOH A 23 1555 1555 2.07 SITE 1 AC1 6 DG A 2 HOH A 21 HOH A 22 HOH A 23 SITE 2 AC1 6 HOH A 24 HOH A 25 CRYST1 44.783 44.783 41.393 90.00 90.00 120.00 P 61 12 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 0.022330 0.012892 0.000000 0.00000 SCALE2 0.000000 0.025784 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024159 0.00000 MASTER 254 0 1 0 0 0 2 6 0 0 0 2 END