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- PDB-4f27: Crystal structures reveal the multi-ligand binding mechanism of t... -

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Basic information

Entry
Database: PDB / ID: 4f27
TitleCrystal structures reveal the multi-ligand binding mechanism of the Staphylococcus aureus ClfB
Components
  • Clumping factor B
  • peptide from Fibrinogen alpha chain
KeywordsCELL ADHESION/BLOOD CLOTTING / Dev-IgG fold / protein-peptide complex / fibronogen / cell surface / cell adhesion-blood clotting 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
: / 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-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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibrinogen alpha chain / Clumping factor B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.917 Å
AuthorsYang, M.J. / Xiang, H. / Wang, J.W. / Liu, B. / Chen, Y.G. / Liu, L. / Deng, X.M. / Feng, Y.
CitationJournal: Plos Pathog. / Year: 2012
Title: Crystal Structures Reveal the Multi-Ligand Binding Mechanism of Staphylococcus aureus ClfB
Authors: Xiang, H. / Feng, Y. / Wang, J.W. / Liu, B. / Chen, Y.G. / Liu, L. / Deng, X.M. / Yang, M.J.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Experimental preparation
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clumping factor B
Q: peptide from Fibrinogen alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2224
Polymers41,1732
Non-polymers492
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-20 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.983, 70.983, 174.908
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Clumping factor B / Fibrinogen receptor B / Fibrinogen-binding protein B


Mass: 40063.094 Da / Num. of mol.: 1 / Fragment: UNP residues 197-542
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: clfB, SAR2709 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GDH2
#2: Protein/peptide peptide from Fibrinogen alpha chain / Fibrinopeptide A / Fibrinogen alpha chain


Mass: 1110.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: P02671
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
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: 3.09 Å3/Da / Density % sol: 60.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate tribasic dehydrate, 20% 2-propanol, 20% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.917→34.783 Å / Num. obs: 45741 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 40.38 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.9166-1.9684174
1.9684-2.0263188
2.0263-2.0917190
2.0917-2.1664193
2.1664-2.2532186
2.2532-2.3557188

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.917→34.783 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 1985 4.99 %
Rwork0.1891 --
obs0.1909 39740 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.1532 Å2
Baniso -1Baniso -2Baniso -3
1-4.7247 Å2-0 Å2-0 Å2
2--4.7247 Å20 Å2
3----9.4493 Å2
Refinement stepCycle: LAST / Resolution: 1.917→34.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 2 116 2754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122683
X-RAY DIFFRACTIONf_angle_d1.3313637
X-RAY DIFFRACTIONf_dihedral_angle_d12.162964
X-RAY DIFFRACTIONf_chiral_restr0.099402
X-RAY DIFFRACTIONf_plane_restr0.006482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9166-1.96450.31391370.292517265495
1.9645-2.01760.30511170.244126972814100
2.0176-2.0770.28051490.21926452794100
2.077-2.1440.21581430.210426632806100
2.144-2.22060.24881270.21962683281099
2.2206-2.30950.29371380.27292579271797
2.3095-2.41460.28671380.223327042842100
2.4146-2.54180.26961370.214727122849100
2.5418-2.7010.23291330.212626992832100
2.701-2.90950.24661600.217326962856100
2.9095-3.20210.28071500.207527372887100
3.2021-3.6650.21651750.191927072882100
3.665-4.61580.1931540.154927662920100
4.6158-34.78840.18311270.158729503077100
Refinement TLS params.Method: refined / Origin x: -35.1062 Å / Origin y: 0.3901 Å / Origin z: -12.9097 Å
111213212223313233
T0.5523 Å2-0.0902 Å2-0.0427 Å2-0.2466 Å20.0056 Å2--0.2754 Å2
L1.1842 °20.2751 °2-0.166 °2-1.4824 °2-0.4097 °2--1.432 °2
S0.0837 Å °-0.181 Å °0.0127 Å °-0.1206 Å °-0.1634 Å °-0.0135 Å °-0.0953 Å °0.0267 Å °0.0997 Å °
Refinement TLS groupSelection details: all

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