10 20 30 40 50 60 70 80 2PLB - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 19-APR-07 2PLB
TITLE D(GTATACC) UNDER HYDROSTATIC PRESSURE OF 1.39 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.KAHN,R.FOURME
REVDAT 4 24-FEB-09 2PLB 1 VERSN REVDAT 3 22-JAN-08 2PLB 1 TITLE COMPND REMARK REVDAT 2 11-SEP-07 2PLB 1 JRNL REVDAT 1 24-JUL-07 2PLB 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 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 (%) : 99.9 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) : 0.219 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.187 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 440 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 5582 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.202 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)) : 4600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 331 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 412.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 178.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1747 REMARK 3 NUMBER OF RESTRAINTS : 1776 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.030 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) : 0.008 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.020 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.063 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: ONE SUGAR AND ONE PHOSPHATE GROUP REMARK 3 ARE DISORDERED (TWO POSITIONS). THE SPERMINE MOLECULE IS ALSO REMARK 3 DISORDERED
REMARK 4 REMARK 4 2PLB 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 RCSB042504.
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, NO REMARK 200 FOCUSING 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 : 5518 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4000 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) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.33100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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 (%): 41.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 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 13.43333 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 26.86667 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 20.15000 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 33.58333 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 6.71667 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. = 1.8 DEGREES REMARK 500 DT A 3 N3 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA A 4 N1 - C2 - N3 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA A 4 C2 - N3 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 DT A 5 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DA A 6 O5' - C5' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DA A 6 N1 - C6 - N6 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC A 7 P - O5' - C5' ANGL. DEV. = 11.9 DEGREES REMARK 500 DC A 7 C6 - N1 - C2 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 6 C3' - O3' - P ANGL. DEV. = 9.7 DEGREES REMARK 500 DA B 4 C2 - N3 - C4 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA B 6 O4' - C4' - C3' ANGL. DEV. = -3.3 DEGREES REMARK 500 DA B 6 N1 - C6 - N6 ANGL. DEV. = 9.8 DEGREES REMARK 500 DA B 6 C5 - C6 - N6 ANGL. DEV. = -8.2 DEGREES REMARK 500 DC B 7 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 175 DISTANCE = 5.37 ANGSTROMS
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: 2PL8 RELATED DB: PDB REMARK 900 D-(GGTATACC) UNDER 1.04 GPA HYDROSTATIC PRESSURE REMARK 900 RELATED ID: 2PLO RELATED DB: PDB REMARK 900 D-(GTATACC) LOW TEMPERATURE (100K)
DBREF 2PLB A 1 8 PDB 2PLB 2PLB 1 8 DBREF 2PLB B 1 8 PDB 2PLB 2PLB 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 SPM B 20 28
HETNAM SPM SPERMINE
FORMUL 3 SPM C10 H26 N4 FORMUL 4 HOH *76(H2 O)
SITE 1 AC1 3 DT B 5 DA B 6 HOH B 133
CRYST1 42.830 42.830 40.300 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 0.023348 0.013480 0.000000 0.00000
SCALE2 0.000000 0.026960 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024814 0.00000