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- PDB-4f20: Crystal structures reveal the multi-ligand binding mechanism of t... -

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Basic information

Entry
Database: PDB / ID: 4f20
TitleCrystal structures reveal the multi-ligand binding mechanism of the Staphylococcus aureus ClfB
Components
  • Clumping factor B
  • peptide from Dermokine
KeywordsCELL ADHESION/CYTOKINE / Dev-IgG fold / protein-peptide complex / Cell Adhesion / Dermokine / Cell Surface / Cell adhesion-Cytokine complex
Function / homology
Function and homology information


cornified envelope assembly / cell adhesion / extracellular space / extracellular region
Similarity search - Function
Dermokine / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / Immunoglobulin-like - #1290 / Immunoglobulin-like - #1280 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / YSIRK type signal peptide / Adhesion domain superfamily ...Dermokine / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / Immunoglobulin-like - #1290 / Immunoglobulin-like - #1280 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / YSIRK type signal peptide / Adhesion domain superfamily / 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
Dermokine / Clumping factor B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 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 1.1Nov 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: Clumping factor B
Q: peptide from Dermokine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0204
Polymers40,9712
Non-polymers492
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-17 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.088, 70.088, 175.760
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: 39875.512 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 Dermokine / / Epidermis-specific secreted protein SK30/SK89


Mass: 1095.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6E0U4
#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 / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.04 Å3/Da / Density % sol: 59.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate tribase dehydrate pH5.6, 20% 2-proparol, 20% polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.502→34.368 Å / Num. obs: 17640 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 64.18 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.5021-2.6588170
2.6588-2.864186
2.864-3.1521193
3.1521-3.6078197
3.6078-4.5438199
4.5438-34.3707198

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F27

4f27


Resolution: 2.502→34.368 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 34.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 892 5.1 %
Rwork0.2239 --
obs0.2261 17507 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.0169 Å2
Baniso -1Baniso -2Baniso -3
1-6.1792 Å2-0 Å2-0 Å2
2--6.1792 Å20 Å2
3----12.3583 Å2
Refinement stepCycle: LAST / Resolution: 2.502→34.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 2 13 2635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032666
X-RAY DIFFRACTIONf_angle_d0.7833611
X-RAY DIFFRACTIONf_dihedral_angle_d13.228958
X-RAY DIFFRACTIONf_chiral_restr0.057397
X-RAY DIFFRACTIONf_plane_restr0.003479
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5021-2.65880.39131440.3586244589
2.6588-2.8640.36581570.2936275499
2.864-3.15210.30841500.2737279299
3.1521-3.60780.29891590.24442792100
3.6078-4.54380.22311540.2022285199
4.5438-34.37070.25451280.1992298198
Refinement TLS params.Method: refined / Origin x: -17.9344 Å / Origin y: 29.8243 Å / Origin z: 13.1066 Å
111213212223313233
T1.0275 Å2-0.4808 Å20.0909 Å2-1.2174 Å2-0.096 Å2--0.4999 Å2
L1.4457 °20.4205 °2-0.0833 °2-2.0054 °2-0.8677 °2--3.5744 °2
S0.1894 Å °-0.3074 Å °0.0428 Å °-0.263 Å °-0.3583 Å °0.0306 Å °0.1247 Å °-0.0247 Å °0.1898 Å °
Refinement TLS groupSelection details: all

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