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- PDB-5h3x: The structure of the N-terminal of the fibronectin/fibrinogen-bin... -

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Basic information

Entry
Database: PDB / ID: 5h3x
TitleThe structure of the N-terminal of the fibronectin/fibrinogen-binding protein from Streptococcus suis (FBPS)
ComponentsFibronectin/fibrinogen binding protein
KeywordsCELL ADHESION / fibronectin-binding property
Function / homology
Function and homology information


ribosomal large subunit binding / rescue of stalled ribosome / tRNA binding / cell adhesion
Similarity search - Function
ibrinogen binding protein from staphylococcus aureus fold / ibrinogen binding protein from staphylococcus aureus domain / fibrinogen binding protein from staphylococcus aureus domain like / Ribonuclease HI; Chain A / NFACT protein RNA binding domain / Rqc2 homolog RqcH, bacterial / NFACT, RNA-binding domain / NFACT protein RNA binding domain / NFACT N-terminal and middle domains / Roll ...ibrinogen binding protein from staphylococcus aureus fold / ibrinogen binding protein from staphylococcus aureus domain / fibrinogen binding protein from staphylococcus aureus domain like / Ribonuclease HI; Chain A / NFACT protein RNA binding domain / Rqc2 homolog RqcH, bacterial / NFACT, RNA-binding domain / NFACT protein RNA binding domain / NFACT N-terminal and middle domains / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Rqc2 homolog RqcH / Rqc2 homolog RqcH
Similarity search - Component
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsMokiMusyoki, A. / 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


Theoretical massNumber of molelcules
Total (without water)30,5971
Polymers30,5971
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14080 Å2
Unit cell
Length a, b, c (Å)70.555, 70.555, 110.183
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 Fibronectin/fibrinogen binding protein


Mass: 30597.449 Da / Num. of mol.: 1 / Fragment: UNP residues 2-268 / Mutation: H28N
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M Na Citrate (pH 5.6), 20%(w/v) PEG 4,000, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 16622 / % possible obs: 97.6 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 29.98
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.512

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Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→33.597 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 23.3
RfactorNum. reflection% reflection
Rfree0.2455 791 5.09 %
Rwork0.216 --
obs0.2175 15547 91.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 33.84 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3498 Å20 Å2-0 Å2
2--4.3498 Å20 Å2
3----8.6995 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 0 129 2288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132204
X-RAY DIFFRACTIONf_angle_d1.2152980
X-RAY DIFFRACTIONf_dihedral_angle_d21.829824
X-RAY DIFFRACTIONf_chiral_restr0.112331
X-RAY DIFFRACTIONf_plane_restr0.008393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.097-2.22830.28781190.25942100X-RAY DIFFRACTION80
2.2283-2.40040.291380.24852333X-RAY DIFFRACTION89
2.4004-2.64180.30841350.24312391X-RAY DIFFRACTION91
2.6418-3.02390.2571290.24592507X-RAY DIFFRACTION94
3.0239-3.80890.24811410.20972625X-RAY DIFFRACTION97
3.8089-33.60180.19411290.18532800X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -3.9158 Å / Origin y: 12.7473 Å / Origin z: 10.2025 Å
111213212223313233
T0.2114 Å2-0.0107 Å2-0.0336 Å2-0.1524 Å2-0.0072 Å2--0.1714 Å2
L1.1289 °2-0.4623 °20.1281 °2-0.6414 °20.0469 °2--0.8324 °2
S-0.0742 Å °-0.0494 Å °0.0041 Å °0.0054 Å °0.0637 Å °-0.0192 Å °-0.0794 Å °0.0391 Å °-0 Å °
Refinement TLS groupSelection details: all

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