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- PDB-6leb: Staphylococcus aureus surface protein SdrC mutant-P366H -

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Basic information

Entry
Database: PDB / ID: 6leb
TitleStaphylococcus aureus surface protein SdrC mutant-P366H
ComponentsSer-Asp rich fibrinogen-binding, bone sialoprotein-binding protein
KeywordsSTRUCTURAL PROTEIN / Dimer
Function / homology
Function and homology information


cell wall / 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 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Ser-Asp rich fibrinogen-binding, bone sialoprotein-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsHang, T. / Zhang, M. / Wang, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Structural insights into the intermolecular interaction of the adhesin SdrC in the pathogenicity of Staphylococcus aureus.
Authors: Wang, J. / Zhang, M. / Wang, M. / Zang, J. / Zhang, X. / Hang, T.
History
DepositionNov 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ser-Asp rich fibrinogen-binding, bone sialoprotein-binding protein
B: Ser-Asp rich fibrinogen-binding, bone sialoprotein-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3229
Polymers70,8132
Non-polymers5097
Water20,5011138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-27 kcal/mol
Surface area28330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.734, 87.130, 63.974
Angle α, β, γ (deg.)90.000, 97.990, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 181 - 495 / Label seq-ID: 1 - 315

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ser-Asp rich fibrinogen-binding, bone sialoprotein-binding protein


Mass: 35406.305 Da / Num. of mol.: 2 / Mutation: P366H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: sdrC / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q2UWK0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.08 M Magnesium formate dihydrate, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 100843 / % possible obs: 99.8 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.096 / Χ2: 10.509 / Net I/σ(I): 3.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.49-1.527.427730.1540.6040.80896.7
1.52-1.5410.128330.3040.470.884100
1.54-1.5711.128770.3070.4141.012100
1.57-1.6111.828790.3590.3691.176100
1.61-1.6412.228740.5250.3451.268100
1.64-1.6812.328620.5020.3161.531100
1.68-1.721228610.520.2991.7271000.999
1.72-1.771328660.5560.2582.311000.9060.942
1.77-1.8213.428940.6380.2363.2051000.8390.872
1.82-1.8813.428750.6840.2284.2761000.810.842
1.88-1.9413.128940.740.2145.7251000.7550.785
1.94-2.0212.628720.7790.2147.7291000.7340.765
2.02-2.1112.929010.6920.20410.1041000.7130.742
2.11-2.2313.728840.8130.19112.0631000.6890.715
2.23-2.3713.629290.8240.18313.5181000.6580.683
2.37-2.5513.229000.8910.17914.8551000.6340.659
2.55-2.813.129200.890.17317.7221000.6110.635
2.8-3.2113.829360.9350.16724.2181000.6090.631
3.21-4.0412.829550.9250.16534.8321000.5750.599
4.04-5013.130880.9330.15235.9381000.550.571

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IRP

3irp


Resolution: 1.54→50 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.071
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1774 5023 5 %RANDOM
Rwork0.1259 ---
obs0.1285 95689 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.67 Å2 / Biso mean: 19.468 Å2 / Biso min: 7.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å20.35 Å2
2--0.89 Å20 Å2
3----0.87 Å2
Refinement stepCycle: final / Resolution: 1.54→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4994 0 32 1138 6164
Biso mean--40.31 35.58 -
Num. residues----630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.025205
X-RAY DIFFRACTIONr_bond_other_d00.024667
X-RAY DIFFRACTIONr_angle_refined_deg2.2551.9257071
X-RAY DIFFRACTIONr_angle_other_deg3.87310770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9195651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63526.496274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32615873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.618158
X-RAY DIFFRACTIONr_chiral_restr0.1530.2789
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.026144
X-RAY DIFFRACTIONr_gen_planes_other0.0290.021244
X-RAY DIFFRACTIONr_rigid_bond_restr10.78739872
X-RAY DIFFRACTIONr_sphericity_free31.159598
X-RAY DIFFRACTIONr_sphericity_bonded10.181510817
Refine LS restraints NCSNumber: 2837 / Type: TIGHT THERMAL / Rms dev position: 2.8 Å / Weight position: 0.5
LS refinement shellResolution: 1.543→1.583 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 323 -
Rwork0.188 6424 -
all-6747 -
obs--89.85 %

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