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- PDB-5cfa: Crystal structures of Bbp from Staphylococcus aureus with peptide... -

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Basic information

Entry
Database: PDB / ID: 5cfa
TitleCrystal structures of Bbp from Staphylococcus aureus with peptide ligand
Components
  • Bone sialoprotein-binding protein
  • Peptide from Fibrinogen alpha chain
KeywordsPROTEIN BINDING/PEPTIDE / Bbp / Fibrinogen / Sdr / MSCRAMM / Staphylococcus aureus / PROTEIN BINDING-PEPTIDE complex
Function / homology
Function and homology information


blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent ...blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein polymerization / Integrin cell surface interactions / Common Pathway of Fibrin Clot Formation / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / fibrinolysis / positive regulation of vasoconstriction / positive regulation of substrate adhesion-dependent cell spreading / Integrin signaling / platelet alpha granule lumen / cell-matrix adhesion / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / response to calcium ion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / Platelet degranulation / extracellular vesicle / ER-Phagosome pathway / protein-containing complex assembly / protein-macromolecule adaptor activity / : / blood microparticle / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / cell adhesion / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / innate immune response / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
SD-repeat containing protein, B domain / SdrD B-like domain / : / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / Immunoglobulin-like - #1290 / SDR-like Ig domain / Bacterial Ig domain / Immunoglobulin-like - #1280 / Fibrinogen alpha C domain ...SD-repeat containing protein, B domain / SdrD B-like domain / : / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / Immunoglobulin-like - #1290 / SDR-like Ig domain / Bacterial Ig domain / Immunoglobulin-like - #1280 / Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrogen-binding domain 1 / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Adhesion domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibrinogen alpha chain / Bone sialoprotein-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsYu, Y. / Zhang, X.Y. / Gu, J.K.
CitationJournal: Protein Cell / Year: 2015
Title: Crystal structures of Bbp from Staphylococcus aureus reveal the ligand binding mechanism with Fibrinogen alpha
Authors: Zhang, X.Y. / Wu, M. / Zhuo, W. / Gu, J.K. / Zhang, S.S. / Ge, J.P. / Yang, M.J.
History
DepositionJul 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bone sialoprotein-binding protein
B: Bone sialoprotein-binding protein
D: Peptide from Fibrinogen alpha chain
C: Peptide from Fibrinogen alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3585
Polymers76,3334
Non-polymers241
Water18,4831026
1
A: Bone sialoprotein-binding protein
C: Peptide from Fibrinogen alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1913
Polymers38,1672
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-12 kcal/mol
Surface area14760 Å2
MethodPISA
2
B: Bone sialoprotein-binding protein
D: Peptide from Fibrinogen alpha chain


Theoretical massNumber of molelcules
Total (without water)38,1672
Polymers38,1672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-4 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.916, 74.961, 75.563
Angle α, β, γ (deg.)90.000, 102.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bone sialoprotein-binding protein / BSP-binding protein


Mass: 36500.008 Da / Num. of mol.: 2 / Fragment: UNP residues 272-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: bbp / Production host: Escherichia coli (E. coli) / References: UniProt: Q14U76
#2: Protein/peptide Peptide from Fibrinogen alpha chain


Mass: 1666.704 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02671
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1026 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: peptide was added into the concentrated protein samples at 10:1 ratio and the protein-peptide complex crystals are grown in 0.2 M lithium sulfate, 0.1M Tris-HCl pH8.2, 30% PEG4000 protein ...Details: peptide was added into the concentrated protein samples at 10:1 ratio and the protein-peptide complex crystals are grown in 0.2 M lithium sulfate, 0.1M Tris-HCl pH8.2, 30% PEG4000 protein concentration was 30mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 116230 / % possible obs: 99.2 % / Redundancy: 5.1 % / Biso Wilson estimate: 16.76 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.041 / Rrim(I) all: 0.093 / Χ2: 1.408 / Net I/av σ(I): 26.812 / Net I/σ(I): 6.9 / Num. measured all: 591166
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.54.50.865111530.7470.4420.9760.82295.8
1.5-1.564.90.728116020.8370.3640.8170.86698.9
1.56-1.635.20.547115340.9020.2680.610.91799.2
1.63-1.725.20.382116170.9470.1870.4260.99299.5
1.72-1.835.20.253116260.9730.1230.2821.06399.6
1.83-1.975.20.16116620.9860.0780.1781.25399.8
1.97-2.175.20.121116920.9890.0590.1351.67699.9
2.17-2.485.20.103117210.9910.050.1152.04100
2.48-3.125.10.071117650.9960.0340.0782.00999.9
3.12-505.30.051118580.9970.0250.0572.24599.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CF3

5cf3


Resolution: 1.45→36.56 Å / FOM work R set: 0.8246 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 5811 5 %
Rwork0.1783 110319 -
obs0.18 116130 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.31 Å2 / Biso mean: 22.46 Å2 / Biso min: 8 Å2
Refinement stepCycle: final / Resolution: 1.45→36.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5223 0 1 1026 6250
Biso mean--13.64 32.26 -
Num. residues----672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075373
X-RAY DIFFRACTIONf_angle_d1.147315
X-RAY DIFFRACTIONf_chiral_restr0.044860
X-RAY DIFFRACTIONf_plane_restr0.005950
X-RAY DIFFRACTIONf_dihedral_angle_d12.7211955
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4499-1.46640.37421600.31693338349890
1.4664-1.48360.32541900.30523585377596
1.4836-1.50170.29152060.28723562376898
1.5017-1.52070.28092080.27313642385099
1.5207-1.54070.31761800.26143655383599
1.5407-1.56180.29861950.25623710390599
1.5618-1.58420.27271670.24833652381999
1.5842-1.60780.28582250.23433635386099
1.6078-1.63290.24191910.21583670386199
1.6329-1.65970.25341730.21623671384499
1.6597-1.68830.25381990.2113706390599
1.6883-1.7190.24311730.20733687386099
1.719-1.75210.26152060.21236813887100
1.7521-1.78780.2492220.20083657387999
1.7878-1.82670.21621830.19936823865100
1.8267-1.86920.22872100.190236843894100
1.8692-1.91590.23681760.181736973873100
1.9159-1.96770.16881860.178537233909100
1.9677-2.02560.20852120.17936713883100
2.0256-2.0910.24561970.181937263923100
2.091-2.16570.20051710.181637093880100
2.1657-2.25240.22441960.182837203916100
2.2524-2.35490.24022210.182136973918100
2.3549-2.47910.20952120.181436913903100
2.4791-2.63440.19451750.177237163891100
2.6344-2.83770.23362050.182137413946100
2.8377-3.12310.24391830.172737423925100
3.1231-3.57470.18251910.154737653956100
3.5747-4.50240.15212210.1336913912100
4.5024-36.57130.17131770.14883813399099

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