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- PDB-5h3w: The structure of the C-terminal of the fibronectin/fibrinogen-bin... -

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Basic information

Entry
Database: PDB / ID: 5h3w
TitleThe structure of the C-terminal of the fibronectin/fibrinogen-binding protein from Streptococcus suis (FBPS)
Components(Fibronectin/fibrinogen binding protein) x 2
KeywordsCELL ADHESION / novel fold / fibronectin-binding property
Function / homology
Function and homology information


RQC complex / ribosomal large subunit binding / rescue of stalled cytosolic ribosome / tRNA binding / cell adhesion / rRNA binding
Similarity search - Function
Rqc2 homolog RqcH, bacterial / : / NFACT, RNA-binding domain / NFACT protein RNA binding domain / NFACT N-terminal and middle domains
Similarity search - Domain/homology
Rqc2 homolog RqcH / Rqc2 homolog RqcH
Similarity search - Component
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMusyoki, A.M. / Qi, J. / Gao, G.F.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Structural and functional analysis of an anchorless fibronectin-binding protein FBPS from Gram-positive bacterium Streptococcus suis
Authors: Musyoki, A.M. / Shi, Z. / Xuan, C. / Lu, G. / Qi, J. / Gao, F. / Zheng, B. / Zhang, Q. / Li, Y. / Haywood, J. / Liu, C. / Yan, J. / Shi, Y. / Gao, G.F.
History
DepositionOct 27, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Mar 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: Fibronectin/fibrinogen binding protein
B: Fibronectin/fibrinogen binding protein


Theoretical massNumber of molelcules
Total (without water)64,7832
Polymers64,7832
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-6 kcal/mol
Surface area28020 Å2
Unit cell
Length a, b, c (Å)40.338, 103.645, 83.278
Angle α, β, γ (deg.)90.00, 92.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fibronectin/fibrinogen binding protein


Mass: 32312.889 Da / Num. of mol.: 1 / Fragment: UNP residues 272-552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Gene: fbps / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RP86, UniProt: A4VWG9*PLUS
#2: Protein Fibronectin/fibrinogen binding protein


Mass: 32470.084 Da / Num. of mol.: 1 / Fragment: UNP residues 271-552 / Mutation: L50I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Gene: fbps / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RP86, UniProt: A4VWG9*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES (pH 7.5), 10%(w/v) PEG 4,000, 500mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 21058 / % possible obs: 97.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 17.57
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.338

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→38.613 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.72
RfactorNum. reflection% reflection
Rfree0.2487 1067 5.08 %
Rwork0.2191 --
obs0.2207 21011 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→38.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4001 0 0 89 4090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014051
X-RAY DIFFRACTIONf_angle_d1.3155428
X-RAY DIFFRACTIONf_dihedral_angle_d17.0311606
X-RAY DIFFRACTIONf_chiral_restr0.072617
X-RAY DIFFRACTIONf_plane_restr0.005692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.68830.2727900.24041990X-RAY DIFFRACTION75
2.6883-2.82990.26751300.23852423X-RAY DIFFRACTION96
2.8299-3.00720.28071500.22382558X-RAY DIFFRACTION100
3.0072-3.23930.28251220.23582590X-RAY DIFFRACTION100
3.2393-3.5650.27221260.20652591X-RAY DIFFRACTION100
3.565-4.08040.26281380.19962597X-RAY DIFFRACTION100
4.0804-5.1390.19881470.20552591X-RAY DIFFRACTION100
5.139-38.61750.24721640.23652604X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.309 Å / Origin y: 19.6585 Å / Origin z: 13.004 Å
111213212223313233
T0.3144 Å20.0012 Å20.0012 Å2-0.2799 Å2-0.0226 Å2--0.2713 Å2
L0.5925 °20.0812 °2-0.1421 °2-0.0097 °2-0.1994 °2--0.2184 °2
S-0.064 Å °-0.0198 Å °-0.0279 Å °-0.0011 Å °0.0071 Å °-0.0074 Å °0.0039 Å °0.0178 Å °-0.0026 Å °
Refinement TLS groupSelection details: all

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