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- PDB-5ihw: The crystal structure of SdrE from staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 5ihw
TitleThe crystal structure of SdrE from staphylococcus aureus
ComponentsSerine-aspartate repeat-containing protein E
KeywordsMEMBRANE PROTEIN / SdrE / virulence factor
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 / Immunoglobulin-like - #1290 / Immunoglobulin-like - #1280 / SDR-like Ig domain / Bacterial Ig domain / : / Fibrogen-binding domain 1 ...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
Serine-aspartate repeat-containing protein E
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsZhang, S. / Wei, J. / Wu, S. / Zhang, X. / Luo, M. / Wang, D.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81301395 China
Chongqing Natural Science Foundationcstc2015jcyjA10003 China
CitationJournal: To Be Published
Title: The crystal structure of SdrE from staphylococcus aureus
Authors: Zhang, S. / Wei, J. / Wu, S. / Zhang, X. / Luo, M. / Wang, D.
History
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine-aspartate repeat-containing protein E


Theoretical massNumber of molelcules
Total (without water)35,1861
Polymers35,1861
Non-polymers00
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.260, 41.560, 51.140
Angle α, β, γ (deg.)95.590, 97.550, 99.550
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Serine-aspartate repeat-containing protein E


Mass: 35185.555 Da / Num. of mol.: 1 / Fragment: UNP residues 273-586
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain MSSA476) (bacteria)
Strain: MSSA476 / Gene: sdrE, SAS0521 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GBS4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2mol/L CaCl2, 35% PEG 3350, 0.1mol/L, Bis-Tris pH 6.6
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9782 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 1.25→50.32 Å / Num. obs: 75580 / % possible obs: 87 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 8.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CF3

5cf3


Resolution: 1.25→50.32 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.343 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.046
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1764 2416 3.2 %RANDOM
Rwork0.1433 ---
obs0.1444 73166 87.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.52 Å2 / Biso mean: 17.096 Å2 / Biso min: 5.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.13 Å20.34 Å2
2---0.55 Å2-0.36 Å2
3---0.2 Å2
Refinement stepCycle: final / Resolution: 1.25→50.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 0 319 2795
Biso mean---25.55 -
Num. residues----314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.022529
X-RAY DIFFRACTIONr_bond_other_d0.0020.022332
X-RAY DIFFRACTIONr_angle_refined_deg2.2631.953432
X-RAY DIFFRACTIONr_angle_other_deg0.95735402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39526.88125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70715448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.121153
X-RAY DIFFRACTIONr_chiral_restr0.1440.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022916
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02543
X-RAY DIFFRACTIONr_mcbond_it2.2211.3561260
X-RAY DIFFRACTIONr_mcbond_other2.2021.3541259
X-RAY DIFFRACTIONr_mcangle_it2.6512.0481575
X-RAY DIFFRACTIONr_rigid_bond_restr6.90834861
X-RAY DIFFRACTIONr_sphericity_free21.636566
X-RAY DIFFRACTIONr_sphericity_bonded12.22655073
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 197 -
Rwork0.173 5392 -
all-5589 -
obs--86.81 %

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