10 20 30 40 50 60 70 80 2PLO - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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