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- PDB-5xgt: Crystal structure of the N-terminal domain of Staphylococcus aure... -

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Basic information

Entry
Database: PDB / ID: 5xgt
TitleCrystal structure of the N-terminal domain of Staphylococcus aureus single-stranded DNA-binding protein SsbA at 1.82 angstrom resolution
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / single-strand DNA binding protein / SsbA
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
Single-stranded DNA-binding protein / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsHuang, Y.H. / Chen, C.J. / Huang, C.Y.
CitationJournal: PLoS ONE / Year: 2017
Title: Staphylococcus aureus single-stranded DNA-binding protein SsbA can bind but cannot stimulate PriA helicase.
Authors: Huang, Y.H. / Guan, H.H. / Chen, C.J. / Huang, C.Y.
History
DepositionApr 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: 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

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Assembly

Deposited unit
A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3823
Polymers25,2902
Non-polymers921
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-12 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.792, 88.792, 57.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 12645.094 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: ED98
Gene: ssb_1, A7U48_3558, AS852_01830, BJI72_0272, EDCC5055_00340, QU38_04380
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D1JHQ1, UniProt: A0A0H3JNP6*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 4000, 100mM HEPES sodium salt pH 7.5, 100mM 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: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.82→30 Å / Num. obs: 23485 / % possible obs: 99.9 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 27.47
Reflection shellResolution: 1.82→1.9 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 4.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X3E

1x3e


Resolution: 1.82→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.812 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23311 1095 5.2 %RANDOM
Rwork0.19323 ---
obs0.19525 20126 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.221 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-0 Å20 Å2
2--0.46 Å20 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 1.82→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 6 109 1766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191672
X-RAY DIFFRACTIONr_bond_other_d0.0020.021593
X-RAY DIFFRACTIONr_angle_refined_deg1.861.9422262
X-RAY DIFFRACTIONr_angle_other_deg0.86733616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9685207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85123.26192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89515280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7211522
X-RAY DIFFRACTIONr_chiral_restr0.1120.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021960
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.022.819834
X-RAY DIFFRACTIONr_mcbond_other3.0212.813833
X-RAY DIFFRACTIONr_mcangle_it4.7874.2051039
X-RAY DIFFRACTIONr_mcangle_other4.7854.2121040
X-RAY DIFFRACTIONr_scbond_it3.7043.413838
X-RAY DIFFRACTIONr_scbond_other3.7023.417839
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8834.9181224
X-RAY DIFFRACTIONr_long_range_B_refined8.44424.0851748
X-RAY DIFFRACTIONr_long_range_B_other8.44723.991706
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 84 -
Rwork0.235 1445 -
obs--99.93 %

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