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- PDB-1qvc: CRYSTAL STRUCTURE ANALYSIS OF SINGLE STRANDED DNA BINDING PROTEIN... -

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Basic information

Entry
Database: PDB / ID: 1qvc
TitleCRYSTAL STRUCTURE ANALYSIS OF SINGLE STRANDED DNA BINDING PROTEIN (SSB) FROM E.COLI
ComponentsSINGLE STRANDED DNA BINDING PROTEIN MONOMER
KeywordsDNA BINDING PROTEIN / BETA-BARREL / SINGLE STRANDED DNA BINDING PROTEIN
Function / homology
Function and homology information


single-stranded DNA-binding protein complex / nucleoid / recombinational repair / replisome / positive regulation of catalytic activity / SOS response / mismatch repair / enzyme activator activity / DNA-templated DNA replication / single-stranded DNA binding ...single-stranded DNA-binding protein complex / nucleoid / recombinational repair / replisome / positive regulation of catalytic activity / SOS response / mismatch repair / enzyme activator activity / DNA-templated DNA replication / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair / identical protein binding / cytosol
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
Single-stranded DNA-binding protein / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsMatsumoto, T. / Morimoto, Y. / Shibata, N. / Shimamoto, N. / Tsukihara, T. / Yasuoka, N.
CitationJournal: J.Biochem.(Tokyo) / Year: 2000
Title: Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by X-Ray structure analysis.
Authors: Matsumoto, T. / Morimoto, Y. / Shibata, N. / Kinebuchi, T. / Shimamoto, N. / Tsukihara, T. / Yasuoka, N.
History
DepositionJul 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2012Group: Other
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 MONOMER
B: SINGLE STRANDED DNA BINDING PROTEIN MONOMER
C: SINGLE STRANDED DNA BINDING PROTEIN MONOMER
D: SINGLE STRANDED DNA BINDING PROTEIN MONOMER


Theoretical massNumber of molelcules
Total (without water)61,8894
Polymers61,8894
Non-polymers00
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-35 kcal/mol
Surface area34690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.369, 62.923, 97.792
Angle α, β, γ (deg.)90.00, 112.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
SINGLE STRANDED DNA BINDING PROTEIN MONOMER


Mass: 15472.161 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P02339, UniProt: P0AGE0*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 288 K / Method: small tubes / pH: 9
Details: SODIUM CHLORIDE, AMMONIUM SULFATE, pH 9.0, SMALL TUBES, temperature 288K
Crystal grow
*PLUS
Temperature: 4, 20 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein11
250 mMTris-HCl11
30.325 M11NaCl
40.3-0.6 Mammonium sulfate11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12881
22811
32811
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-310.945
SYNCHROTRONPhoton Factory BL-6A21
SYNCHROTRONPhoton Factory BL-6A31
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJan 19, 1997
FUJI2IMAGE PLATEJul 6, 1996
FUJI3IMAGE PLATENov 7, 1996
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9451
211
ReflectionResolution: 2.2→52 Å / Num. all: 150790 / Num. obs: 24956 / % possible obs: 82.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 39.15 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.8
Reflection shellResolution: 2.2→2.37 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.197 / % possible all: 43.5
Reflection
*PLUS
Num. measured all: 150790
Reflection shell
*PLUS
% possible obs: 43.5 %

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Processing

Software
NameClassification
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.2→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH, R. A. AND HUBER, R.
RfactorNum. reflection% reflectionSelection details
Rfree0.317 1208 -RANDOM
Rwork0.247 ---
obs0.247 23711 83.2 %-
all-23711 --
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4293 0 0 455 4748
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006282
X-RAY DIFFRACTIONc_angle_d1.18855
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 24884 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 66.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0062
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_mcbond_it1.8
X-RAY DIFFRACTIONc_scbond_it2.1
X-RAY DIFFRACTIONc_mcangle_it3.2
X-RAY DIFFRACTIONc_scangle_it3

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