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- PDB-6poo: Novel structure of the N-terminal helical domain of BibA, a group... -

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Basic information

Entry
Database: PDB / ID: 6poo
TitleNovel structure of the N-terminal helical domain of BibA, a group B streptococcus immunogenic bacterial adhesin
ComponentsBibA
KeywordsIMMUNE SYSTEM / BibA / immunogenic / bacteria / adhesin / group B streptococcus
Function / homology
Function and homology information


: / BibA adhesin stalk domain / : / M protein-type anchor domain / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
BibA / Pathogenicity protein, putative
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.03 Å
AuthorsManne, K. / Narayana, S.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Novel structure of the N-terminal helical domain of BibA, a group B streptococcus immunogenic bacterial adhesin.
Authors: Manne, K. / Chattopadhyay, D. / Agarwal, V. / Blom, A.M. / Khare, B. / Chakravarthy, S. / Chang, C. / Ton-That, H. / Narayana, S.V.L.
History
DepositionJul 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BibA


Theoretical massNumber of molelcules
Total (without water)30,9711
Polymers30,9711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.419, 68.814, 199.377
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein BibA / Putative cell-wall anchored surface adhesin


Mass: 30970.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: gbs2018 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0E798, UniProt: Q8DWZ6*PLUS
Has ligand of interestN
Has protein modificationY

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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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.0, 0.2 M Magnesium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97959 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 29, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 3.03→49.85 Å / Num. obs: 7702 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.02811 / Rrim(I) all: 0.03976 / Net I/σ(I): 16.1
Reflection shellResolution: 3.03→3.138 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1893 / Mean I/σ(I) obs: 3.46 / Num. unique obs: 737 / CC1/2: 0.905 / Rrim(I) all: 0.2678 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15.2-3472)refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: MAD / Resolution: 3.03→49.844 Å / SU ML: 0.43 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.55
RfactorNum. reflection% reflection
Rfree0.2395 809 5.92 %
Rwork0.1921 --
obs0.195 7699 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.03→49.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 0 0 2158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112176
X-RAY DIFFRACTIONf_angle_d1.0872912
X-RAY DIFFRACTIONf_dihedral_angle_d18.8491385
X-RAY DIFFRACTIONf_chiral_restr0.058332
X-RAY DIFFRACTIONf_plane_restr0.005376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0301-3.21990.34461390.29032167X-RAY DIFFRACTION100
3.2199-3.46850.25761320.23532125X-RAY DIFFRACTION100
3.4685-3.81740.29881380.2132173X-RAY DIFFRACTION100
3.8174-4.36960.22991360.16592138X-RAY DIFFRACTION100
4.3696-5.50410.2121280.1772113X-RAY DIFFRACTION100
5.5041-49.8440.20971360.17492135X-RAY DIFFRACTION100

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