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- PDB-5wta: Crystal Structure of Staphylococcus aureus SdrE apo form -

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Basic information

Entry
Database: PDB / ID: 5wta
TitleCrystal Structure of Staphylococcus aureus SdrE apo form
ComponentsSerine-aspartate repeat-containing protein E
KeywordsCELL ADHESION / Surface protein / Staphylococcus aureus / Sdr family / complement evasion
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 / YSIRK type signal peptide ...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 / 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 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: 2.3 Å
AuthorsWu, M. / Zhang, Y. / Hang, T. / Wang, C. / Yang, Y. / Zang, J. / Zhang, M. / Zhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Biochem. J. / Year: 2017
Title: Staphylococcus aureus SdrE captures complement factor H's C-terminus via a novel 'close, dock, lock and latch' mechanism for complement evasion
Authors: Zhang, Y. / Wu, M. / Hang, T. / Wang, C. / Yang, Y. / Pan, W. / Zang, J. / Zhang, M. / Zhang, X.
History
DepositionDec 10, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 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

Downloads & links

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Assembly

Deposited unit
A: Serine-aspartate repeat-containing protein E
B: Serine-aspartate repeat-containing protein E
C: Serine-aspartate repeat-containing protein E
D: Serine-aspartate repeat-containing protein E


Theoretical massNumber of molelcules
Total (without water)150,7774
Polymers150,7774
Non-polymers00
Water11,656647
1
A: Serine-aspartate repeat-containing protein E


Theoretical massNumber of molelcules
Total (without water)37,6941
Polymers37,6941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine-aspartate repeat-containing protein E


Theoretical massNumber of molelcules
Total (without water)37,6941
Polymers37,6941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Serine-aspartate repeat-containing protein E


Theoretical massNumber of molelcules
Total (without water)37,6941
Polymers37,6941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Serine-aspartate repeat-containing protein E


Theoretical massNumber of molelcules
Total (without water)37,6941
Polymers37,6941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.810, 61.730, 139.610
Angle α, β, γ (deg.)80.89, 89.83, 73.34
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 37694.152 Da / Num. of mol.: 4 / Fragment: Ligand binding A domain, UNP residues 270-599 / Mutation: I489M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: sdrE, SAV0563 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q932F7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 647 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M Citric acid, pH 3.5, 16% PEG 3350 (w/v), 2% MPD (v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→40.01 Å / Num. obs: 55992 / % possible obs: 95.5 % / Redundancy: 2.2 % / Rsym value: 0.08 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 8137 / Rsym value: 0.26 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R17

1r17


Resolution: 2.3→38.93 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.882 / Cross valid method: THROUGHOUT / ESU R: 0.454 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25171 2821 5 %RANDOM
Rwork0.19409 ---
obs0.19693 53169 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.278 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.05 Å20.4 Å2
2---0.08 Å2-0.88 Å2
3----0.78 Å2
Refinement stepCycle: 1 / Resolution: 2.3→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9900 0 0 647 10547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0210082
X-RAY DIFFRACTIONr_bond_other_d00.029292
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.94713693
X-RAY DIFFRACTIONr_angle_other_deg3.703321506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27551262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.97626.978503
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.292151766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9751512
X-RAY DIFFRACTIONr_chiral_restr0.0840.21570
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211678
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022178
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7132.1375036
X-RAY DIFFRACTIONr_mcbond_other1.7122.1375035
X-RAY DIFFRACTIONr_mcangle_it2.6783.2016290
X-RAY DIFFRACTIONr_mcangle_other2.6783.2016291
X-RAY DIFFRACTIONr_scbond_it2.3672.3155046
X-RAY DIFFRACTIONr_scbond_other2.3672.3155046
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6323.3957400
X-RAY DIFFRACTIONr_long_range_B_refined5.20917.29711344
X-RAY DIFFRACTIONr_long_range_B_other5.13317.22711224
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 219 -
Rwork0.23 3928 -
obs--95.09 %

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