10 20 30 40 50 60 70 80 2PL8 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 19-APR-07 2PL8
TITLE D(GTATACC) UNDER HYDROSTATIC PRESSURE OF 1.04 GPA
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: SYNTHETIC DNA OCTAMER
KEYWDS DNA, HIGH-PRESSURE, CRYSTAL STRUCTURE
EXPDTA X-RAY DIFFRACTION
AUTHOR T.PRANGE,E.GIRARD,R.FOURME,R.KAHN
REVDAT 4 24-FEB-09 2PL8 1 VERSN REVDAT 3 22-JAN-08 2PL8 1 TITLE COMPND REMARK REVDAT 2 11-SEP-07 2PL8 1 JRNL REVDAT 1 24-JUL-07 2PL8 0
JRNL AUTH E.GIRARD,T.PRANGE,A.C.DHAUSSY,E.MIGIANU-GRIFFONI, JRNL AUTH 2 M.LECOUVEY,J.C.CHERVIN,M.MEZOUAR,R.KAHN,R.FOURME JRNL TITL ADAPTATION OF THE BASE-PAIRED DOUBLE-HELIX JRNL TITL 2 MOLECULAR ARCHITECTURE TO EXTREME PRESSURE. JRNL REF NUCLEIC ACIDS RES. V. 35 4800 2007 JRNL REFN ISSN 0305-1048 JRNL PMID 17617642 JRNL DOI 10.1093/NAR/GKM511
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.DOUCET,J.-P.BENOIT,W.B.T.CRUSE,T.PRANGE,O.KENNARD REMARK 1 TITL COEXISTENCE OF A-AND B-FORM DNA IN A SINGLE REMARK 1 TITL 2 CRYSTAL LATTICE REMARK 1 REF NATURE V. 337 190 1989 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 2911354 REMARK 1 DOI 10.1038/337190A0 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.FOURME,R.KAHN,M.MEZOUAR,E.GIRARD,C.HORENTRUP, REMARK 1 AUTH 2 T.PRANGE,I.ASCONE REMARK 1 TITL HIGH-PRESSURE PROTEIN CRYSTALLOGRAPHY (HPPX): REMARK 1 TITL 2 INSTRUMENTATION, METHODOLOGY AND RESULTS ON REMARK 1 TITL 3 LYSOZYME CRYSTALS REMARK 1 REF J.SYNCHROTRON RADIA. V. 8 1149 2001 REMARK 1 REFN ISSN 0909-0495 REMARK 1 PMID 11524565 REMARK 1 DOI 10.1107/S0909049501011037 REMARK 1 REFERENCE 3 REMARK 1 AUTH N.COLLOC'H,E.GIRARD,A.C.DHAUSSY,R.KAHN,I.ASCONE, REMARK 1 AUTH 2 M.MEZOUAR,R.FOURME REMARK 1 TITL HIGH PRESSURE MACROMOLECULAR CRYSTALLOGRAPHY: THE REMARK 1 TITL 2 140 MPA CRYSTAL STRUCTURE AT 2.3 A RESOLUTION OF REMARK 1 TITL 3 URATE OXIDASE, A 135 KD TETRAMERIC ASSEMBLY REMARK 1 REF BIOCHEM.BIOPHYS.ACTA V.1764 391 2006 REMARK 1 REF 2 PROTEINS & PROTEOMICS REMARK 1 REFN ISSN 1570-9639 REMARK 1 PMID 16478683 REMARK 1 DOI 10.1016/J.BBAPAP.2006.01.006 REMARK 1 REFERENCE 4 REMARK 1 AUTH C.E.KUNDROT,F.M.RICHARDS REMARK 1 TITL CRYSTAL STRUCTURE OF HEN EGG-WHITE LYSOZYME AT A REMARK 1 TITL 2 HYDROSTATIC PRESSURE OF 1000 ATMOSPHERES. REMARK 1 REF J.MOL.BIOL. V. 193 157 1987 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 3586017 REMARK 1 DOI 10.1016/0022-2836(87)90634-6
REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 3 CROSS-VALIDATION METHOD : FREE R 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) : 0.206 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.189 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 377 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 5079 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.193 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.189 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 378 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 4171 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 : 14 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 406.80 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 184.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1671 REMARK 3 NUMBER OF RESTRAINTS : 1688 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.027 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) : 0.007 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.018 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.061 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 : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2PL8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-APR-07. REMARK 100 THE RCSB ID CODE IS RCSB042501.
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) : 295 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 : ID27 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.3738 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : 2 CRYSTALS, PARALLEL BEAM REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5018 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 18.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.25100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 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: 2PL4 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MG OF DNA DISSOLVED IN 0.2 ML OF REMARK 280 15% MPD SOLUTION CACODYLATE BUFFER 10-2 M. ADDITIVES: 10-5 M REMARK 280 SODIUM AZIDE, 10-2 M MGCL2, 2.10-2 M SPERMINE CHLORIDE. REMARK 280 RESERVOIR: SAME SOLUTION BUT 50 % MPD, PH 7, VAPOR DIFFUSION, REMARK 280 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 13.48333 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 26.96667 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 20.22500 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 33.70833 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 6.74167 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA B 16 N1 - C6 - N6 ANGL. DEV. = 5.4 DEGREES REMARK 500 DA B 16 C5 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPM B 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: 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 2PL8 A 1 8 PDB 2PL8 2PL8 1 8 DBREF 2PL8 B 11 18 PDB 2PL8 2PL8 11 18
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 SPM B 20 14
HETNAM SPM SPERMINE
FORMUL 3 SPM C10 H26 N4 FORMUL 4 HOH *74(H2 O)
SITE 1 AC1 2 DT B 15 DA B 16
CRYST1 43.423 43.423 40.450 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 0.023029 0.013296 0.000000 0.00000
SCALE2 0.000000 0.026592 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024722 0.00000