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- PDB-5h6i: Crystal Structure of GBS CAMP Factor -

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Basic information

Entry
Database: PDB / ID: 5h6i
TitleCrystal Structure of GBS CAMP Factor
ComponentsProtein B
KeywordsTOXIN / Pore forming toxin
Function / homologyCAMP factor / CAMP factor (Cfa) / IgG binding / extracellular region / Protein B
Function and homology information
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsJin, T.C. / Brefo-Mensah, E.K.
CitationJournal: J.Biol.Chem. / Year: 2018
Title: Crystal structure of theStreptococcus agalactiaeCAMP factor provides insights into its membrane-permeabilizing activity.
Authors: Jin, T. / Brefo-Mensah, E. / Fan, W. / Zeng, W. / Li, Y. / Zhang, Y. / Palmer, M.
History
DepositionNov 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 20, 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

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Assembly

Deposited unit
A: Protein B
B: Protein B
C: Protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4367
Polymers81,1123
Non-polymers3244
Water63135
1
A: Protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2654
Polymers27,0371
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein B


Theoretical massNumber of molelcules
Total (without water)27,0371
Polymers27,0371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1342
Polymers27,0371
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.950, 116.050, 72.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-301-

SO4

21A-302-

SO4

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Components

#1: Protein Protein B / cAMP factor


Mass: 27037.498 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P09879
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2M NH4NO3, 20% PEG 3350, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 54560 / % possible obs: 99.6 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.4
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2.34 / CC1/2: 0.784 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIXdev_2481refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→48.917 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.96
RfactorNum. reflection% reflection
Rfree0.285 3779 6.93 %
Rwork0.2337 --
obs0.2372 54560 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→48.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4956 0 28 35 5019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025033
X-RAY DIFFRACTIONf_angle_d0.4356821
X-RAY DIFFRACTIONf_dihedral_angle_d5.0523135
X-RAY DIFFRACTIONf_chiral_restr0.035840
X-RAY DIFFRACTIONf_plane_restr0.003871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4502-2.48120.42281360.39321795X-RAY DIFFRACTION96
2.4812-2.51380.42531400.33921876X-RAY DIFFRACTION100
2.5138-2.54830.32771380.33511858X-RAY DIFFRACTION100
2.5483-2.58470.38171440.3061942X-RAY DIFFRACTION100
2.5847-2.62330.36761390.31291843X-RAY DIFFRACTION100
2.6233-2.66420.3971360.3171889X-RAY DIFFRACTION100
2.6642-2.70790.37851420.30251903X-RAY DIFFRACTION100
2.7079-2.75460.42951360.30361855X-RAY DIFFRACTION100
2.7546-2.80470.38561440.29691898X-RAY DIFFRACTION100
2.8047-2.85860.28821430.28961881X-RAY DIFFRACTION100
2.8586-2.9170.34431420.30021937X-RAY DIFFRACTION100
2.917-2.98040.37731360.28961825X-RAY DIFFRACTION100
2.9804-3.04970.30421410.31391917X-RAY DIFFRACTION100
3.0497-3.1260.33261430.29041883X-RAY DIFFRACTION100
3.126-3.21050.36821410.27781866X-RAY DIFFRACTION100
3.2105-3.30490.33291410.27311881X-RAY DIFFRACTION100
3.3049-3.41160.34121410.26611884X-RAY DIFFRACTION100
3.4116-3.53350.35531380.25981874X-RAY DIFFRACTION100
3.5335-3.67490.2551420.24531889X-RAY DIFFRACTION100
3.6749-3.84210.28361360.22861887X-RAY DIFFRACTION100
3.8421-4.04460.25351420.21791880X-RAY DIFFRACTION100
4.0446-4.29780.28471390.1961908X-RAY DIFFRACTION100
4.2978-4.62940.26181400.19141861X-RAY DIFFRACTION100
4.6294-5.09490.25261420.18811902X-RAY DIFFRACTION100
5.0949-5.83110.26351380.22241872X-RAY DIFFRACTION100
5.8311-7.34260.27141390.22791899X-RAY DIFFRACTION100
7.3426-48.92720.16811400.15461876X-RAY DIFFRACTION100

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