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- PDB-2vw9: Single stranded DNA binding protein complex from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 2vw9
TitleSingle stranded DNA binding protein complex from Helicobacter pylori
Components
  • POLY-DT
  • SINGLE-STRANDED DNA BINDING PROTEIN
KeywordsDNA BINDING PROTEIN / DNA REPLICATION / SINGLE-STRANDED DNA / SINGLE-STRANDED DNA BINDING PROTEIN / OLIGONUCLEOTIDE/OLIGOSACCHARIDE BINDING FOLD / HELICOBACTER PYLORI / OB-FOLD / DNA DAMAGE / DNA REPAIR / DNA-BINDING PROTEIN
Function / homology
Function and homology information


nucleoid / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair
Similarity search - Function
Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChan, K.-W. / Wang, C.-H. / Lee, Y.-J. / Sun, Y.-J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Single-Stranded DNA-Binding Protein Complex from Helicobacter Pylori Suggests an Ssdna-Binding Surface.
Authors: Chan, K.-W. / Lee, Y.-J. / Wang, C.-H. / Huang, H. / Sun, Y.-J.
History
DepositionJun 18, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "BA" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SINGLE-STRANDED DNA BINDING PROTEIN
B: SINGLE-STRANDED DNA BINDING PROTEIN
C: POLY-DT


Theoretical massNumber of molelcules
Total (without water)40,5403
Polymers40,5403
Non-polymers00
Water2,882160
1
A: SINGLE-STRANDED DNA BINDING PROTEIN
B: SINGLE-STRANDED DNA BINDING PROTEIN
C: POLY-DT

A: SINGLE-STRANDED DNA BINDING PROTEIN
B: SINGLE-STRANDED DNA BINDING PROTEIN
C: POLY-DT


Theoretical massNumber of molelcules
Total (without water)81,0796
Polymers81,0796
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5880 Å2
ΔGint-68.3 kcal/mol
Surface area31170 Å2
MethodPQS
Unit cell
Length a, b, c (Å)75.562, 75.562, 117.691
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SINGLE-STRANDED DNA BINDING PROTEIN / SSB / HELIX-DESTABILIZING PROTEIN


Mass: 14968.873 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG13009 / References: UniProt: O25841
#2: DNA chain POLY-DT


Mass: 10601.791 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: SODIUM CITRATE BUFFER PH5.5, 1.0 M LI2SO4 AND 0.5 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 17468 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 51.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EYG

1eyg


Resolution: 2.3→25.13 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 42178.93 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: BULK SOLVENT MODEL USED MISSING REGIONS CHAIN A RESIDUES 1109-1134 CHAIN B RESIDUES 2106-2134 SSDNA 6, 10-13, 17, 27-29, 34-35 FOLLOW RESIDUES ARE REPLACED TO ALA CHAIN A K1038, K1039, K1108 ...Details: BULK SOLVENT MODEL USED MISSING REGIONS CHAIN A RESIDUES 1109-1134 CHAIN B RESIDUES 2106-2134 SSDNA 6, 10-13, 17, 27-29, 34-35 FOLLOW RESIDUES ARE REPLACED TO ALA CHAIN A K1038, K1039, K1108 CHAIN B K2038, K2039, D2041
RfactorNum. reflection% reflectionSelection details
Rfree0.26 784 4.9 %RANDOM
Rwork0.238 ---
obs0.238 15951 89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.1119 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 49.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.28 Å20 Å20 Å2
2--3.28 Å20 Å2
3----6.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→25.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 465 0 160 2272
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d32.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.57
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.221 100 4.5 %
Rwork0.241 2119 -
obs--76.3 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: WATER_REP.PARAM

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