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- PDB-3o9o: Crystal Structure of GBS1074, an Esat-6 homologue from Group B St... -

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Basic information

Entry
Database: PDB / ID: 3o9o
TitleCrystal Structure of GBS1074, an Esat-6 homologue from Group B Streptococcus
ComponentsUncharacterized protein gbs1074
KeywordsUNKNOWN FUNCTION / WXG100 / 4-Helix Bundle / Putative virulence factor / Putative secreted protein
Function / homologyESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / ESAT-6-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / ESAT-6-like protein
Function and homology information
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsWhite, S.A. / Shukla, A. / Anthony, M.
CitationJournal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2010
Title: The homodimeric GBS1074 from Streptococcus agalactiae.
Authors: Shukla, A. / Pallen, M. / Anthony, M. / White, S.A.
History
DepositionAug 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein gbs1074
B: Uncharacterized protein gbs1074


Theoretical massNumber of molelcules
Total (without water)24,2002
Polymers24,2002
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-38 kcal/mol
Surface area10770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.220, 76.220, 151.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-113-

HOH

21B-142-

HOH

31B-154-

HOH

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Components

#1: Protein Uncharacterized protein gbs1074


Mass: 12100.233 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: NEM316 / Gene: gbs1074 / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: Q8E5F8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 0.75 M LiSO4, 0.6 M (NH4)2SO4, 0.1 M Na citrate, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→40.08 Å / Num. all: 18310 / Num. obs: 18255 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 38.383 Å2 / Rsym value: 0.042 / Net I/σ(I): 34

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Processing

Software
NameClassification
MxCuBEdata collection
SOLVEphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2→40.08 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2192 -RANDOM
Rwork0.189 --
obs0.1906 18255 -
all-18296 -
Displacement parametersBiso mean: 45.936 Å2
Refinement stepCycle: LAST / Resolution: 2→40.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 0 140 1616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_deg0.742

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