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- PDB-5yuo: Crystal structure of SSB protein from Pseudomonas aeruginosa PAO1 -

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Basic information

Entry
Database: PDB / ID: 5yuo
TitleCrystal structure of SSB protein from Pseudomonas aeruginosa PAO1
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / single-strand DNA binding protein / Pseudomonas aeruginosa
Function / homology
Function and homology information


nucleoid / enzyme activator activity / 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
Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.037 Å
AuthorsHuang, Y.H. / Huang, C.Y.
CitationJournal: RSC Adv. / Year: 2018
Title: The glycine-rich flexible region in SSB is crucial for PriA stimulation.
Authors: Huang, Y.H. / Huang, C.Y.
History
DepositionNov 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Single-stranded DNA-binding protein
C: Single-stranded DNA-binding protein
D: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2826
Polymers55,0974
Non-polymers1842
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-11 kcal/mol
Surface area21990 Å2
Unit cell
Length a, b, c (Å)102.208, 64.104, 97.103
Angle α, β, γ (deg.)90.00, 112.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-223-

HOH

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Components

#1: Protein
Single-stranded DNA-binding protein / SSB


Mass: 13774.341 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: ssb, PA4232 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P40947
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% PEG 4000, 100mM HEPES pH 7.0, 50mM sodium acetate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.037→30 Å / Num. obs: 36409 / % possible obs: 98.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 31.36
Reflection shellResolution: 2.04→2.11 Å / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.53 / Num. unique obs: 3312 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EYG

1eyg


Resolution: 2.037→26.49 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.44
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 1826 5.02 %RANDOM
Rwork0.2175 ---
obs0.2196 36399 97.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.037→26.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 12 87 3323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073281
X-RAY DIFFRACTIONf_angle_d0.8444423
X-RAY DIFFRACTIONf_dihedral_angle_d19.4471923
X-RAY DIFFRACTIONf_chiral_restr0.062480
X-RAY DIFFRACTIONf_plane_restr0.004579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0369-2.0920.33061300.30832317X-RAY DIFFRACTION86
2.092-2.15350.34261310.27742605X-RAY DIFFRACTION95
2.1535-2.2230.28841450.26792616X-RAY DIFFRACTION98
2.223-2.30240.30041170.25172701X-RAY DIFFRACTION99
2.3024-2.39450.27791410.24862677X-RAY DIFFRACTION100
2.3945-2.50340.3071510.2462683X-RAY DIFFRACTION100
2.5034-2.63530.27531310.25122727X-RAY DIFFRACTION100
2.6353-2.80020.31621370.25532686X-RAY DIFFRACTION100
2.8002-3.01620.31731380.24812727X-RAY DIFFRACTION100
3.0162-3.31920.3071460.2322687X-RAY DIFFRACTION100
3.3192-3.79830.25271420.20832724X-RAY DIFFRACTION100
3.7983-4.78080.24211400.18282714X-RAY DIFFRACTION100
4.7808-26.49260.20231770.19322709X-RAY DIFFRACTION98

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