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- PDB-5cf3: Crystal structures of Bbp from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 5cf3
TitleCrystal structures of Bbp from Staphylococcus aureus
ComponentsBone sialoprotein-binding protein
KeywordsPROTEIN BINDING / Bbp / Fibrinogen / Sdr / MSCRAMM
Function / homology
Function and homology information


cell adhesion / extracellular region
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 / Immunoglobulin-like - #1280 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily ...SD-repeat containing protein, B domain / SdrD B-like domain / 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 / 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
Bone sialoprotein-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.031 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_conn_angle / pdbx_struct_oper_list / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bone sialoprotein-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5803
Polymers36,5001
Non-polymers802
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-9 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.241, 98.924, 102.257
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-570-

HOH

21A-642-

HOH

31A-658-

HOH

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Components

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


Mass: 36500.008 Da / Num. of mol.: 1 / Fragment: UNP residues 272-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: TCH60 / Gene: bbp / Production host: Escherichia coli (E. coli) / References: UniProt: Q14U76
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 3.48 Å3/Da / Density % sol: 64.61 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: crystals were grown in 0.2 M calcium acetate hydrate, 0.1 M sodium cacodylate trihydrate pH6.5, 18% PEG8000 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: Aug 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 31074 / % possible obs: 96.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 30.12 Å2 / Rmerge(I) obs: 0.078 / Χ2: 1.121 / Net I/av σ(I): 15.602 / Net I/σ(I): 12 / Num. measured all: 115200
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.03-2.13.50.44828321.05889.3
2.1-2.193.60.37531521.05399.9
2.19-2.293.70.26531641.253100
2.29-2.413.70.26631851.20499.9
2.41-2.563.80.17131781.164100
2.56-2.763.90.12831891.137100
2.76-3.033.90.09731931.072100
3.03-3.473.80.06932031.09599.5
3.47-4.373.40.05127371.04284.2
4.37-503.70.04232411.10795.9

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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: 4F24

4f24


Resolution: 2.031→28.593 Å / FOM work R set: 0.7493 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2535 1580 5.09 %
Rwork0.2166 29455 -
obs0.2185 31035 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.84 Å2 / Biso mean: 39.37 Å2 / Biso min: 25.09 Å2
Refinement stepCycle: final / Resolution: 2.031→28.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 2 172 2637
Biso mean--34.69 41.51 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072503
X-RAY DIFFRACTIONf_angle_d1.0973404
X-RAY DIFFRACTIONf_chiral_restr0.044399
X-RAY DIFFRACTIONf_plane_restr0.005441
X-RAY DIFFRACTIONf_dihedral_angle_d14.053911
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0309-2.09650.31641220.2942659278197
2.0965-2.17140.32241550.271426532808100
2.1714-2.25830.48771570.343427252882100
2.2583-2.3610.36181450.285626912836100
2.361-2.48540.29241470.234427122859100
2.4854-2.6410.24541550.227327212876100
2.641-2.84480.27631460.23227442890100
2.8448-3.13070.26281600.224727152875100
3.1307-3.5830.23491280.21822692282097
3.583-4.51130.18681230.17232339246284
4.5113-28.59590.19761420.16932804294697

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