10 20 30 40 50 60 70 80 2PKV - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 18-APR-07 2PKV
TITLE D-(GGTATACC) AMBIENT PRESSURE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC DNA
KEYWDS HIGH PRESSURE, DNA, CRYSTAL STRUCTURE
EXPDTA X-RAY DIFFRACTION
AUTHOR E.GIRARD,T.PRANGE,R.KAHN,R.FOURME
REVDAT 3 24-FEB-09 2PKV 1 VERSN REVDAT 2 11-SEP-07 2PKV 1 JRNL REVDAT 1 24-JUL-07 2PKV 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 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) : 0.159 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.151 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 497 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 6228 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.149 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)) : 5465 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 : 0 REMARK 3 SOLVENT ATOMS : 57 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 379.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 184.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1523 REMARK 3 NUMBER OF RESTRAINTS : 1585 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.029 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) : 0.010 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.006 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.043 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 2PKV 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 RCSB042488.
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 : NULL 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 : 6228 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 19.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 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: 115D FROM PDB REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG OF LYOPHILIZED DNA DISSOLVED REMARK 280 IN 0.2 ML OF A 15 % MPD SOLUTION WITH ADDITIVES: 10-5 M SODIUM REMARK 280 AZIDE, 10-2 M MGCL2 AND 2.10-2 SPERMINE CHLORIDE. RESERVOIR : REMARK 280 SAME SOLUTION BUT 50 % MPD, PH 7, VAPOR DIFFUSION, SITTING REMARK 280 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 13.91667 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 27.83333 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 20.87500 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 34.79167 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 6.95833 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: THE BIOLOGICAL ASSEMBLY IS A DIMER
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 DT A 3 N3 - C2 - O2 ANGL. DEV. = 5.9 DEGREES REMARK 500 DA A 4 C2 - N3 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 DC A 7 C6 - N1 - C2 ANGL. DEV. = 4.9 DEGREES REMARK 500 DC A 7 C2 - N3 - C4 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC A 7 N3 - C4 - C5 ANGL. DEV. = 5.2 DEGREES REMARK 500 DC A 7 C5 - C6 - N1 ANGL. DEV. = -4.0 DEGREES REMARK 500 DC A 7 N3 - C4 - N4 ANGL. DEV. = -4.6 DEGREES REMARK 500 DC A 8 C6 - N1 - C2 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC A 8 N3 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG B 1 C2 - N3 - C4 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG B 1 N3 - C4 - C5 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 1 C5 - C6 - N1 ANGL. DEV. = -3.3 DEGREES REMARK 500 DG B 2 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG B 2 C5 - C6 - O6 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA B 4 N1 - C2 - N3 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA B 4 C8 - N9 - C4 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT B 5 N3 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC B 7 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL
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: 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 2PKV A 1 8 PDB 2PKV 2PKV 1 8 DBREF 2PKV B 1 8 PDB 2PKV 2PKV 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
FORMUL 3 HOH *57(H2 O)
CRYST1 45.030 45.030 41.750 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 0.022207 0.012821 0.000000 0.00000
SCALE2 0.000000 0.025643 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023952 0.00000