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- PDB-5wtb: Complex Structure of Staphylococcus aureus SdrE with human comple... -

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Basic information

Entry
Database: PDB / ID: 5wtb
TitleComplex Structure of Staphylococcus aureus SdrE with human complement factor H
Components
  • Peptide from Complement factor H
  • Serine-aspartate repeat-containing protein E
KeywordsCELL ADHESION / Staphylococcus aureus / Sdr family / complement factor H / complement evasion
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / symbiont cell surface / regulation of complement-dependent cytotoxicity / regulation of complement activation / complement component C3b binding / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation / complement activation, alternative pathway / Regulation of Complement cascade ...regulation of complement activation, alternative pathway / symbiont cell surface / regulation of complement-dependent cytotoxicity / regulation of complement activation / complement component C3b binding / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / heparin binding / blood microparticle / cell adhesion / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
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 / : ...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 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP 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
Complement factor H / Serine-aspartate repeat-containing protein E
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWu, M. / Zhang, Y. / Hang, T. / Wang, C. / Yang, Y. / Zang, J. / Zhang, M. / Zhang, X.
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
D: Serine-aspartate repeat-containing protein E
A: Serine-aspartate repeat-containing protein E
B: Serine-aspartate repeat-containing protein E
C: Serine-aspartate repeat-containing protein E
E: Peptide from Complement factor H
F: Peptide from Complement factor H
G: Peptide from Complement factor H
H: Peptide from Complement factor H


Theoretical massNumber of molelcules
Total (without water)160,8248
Polymers160,8248
Non-polymers00
Water00
1
D: Serine-aspartate repeat-containing protein E
H: Peptide from Complement factor H


Theoretical massNumber of molelcules
Total (without water)40,2062
Polymers40,2062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-9 kcal/mol
Surface area15710 Å2
MethodPISA
2
A: Serine-aspartate repeat-containing protein E
E: Peptide from Complement factor H


Theoretical massNumber of molelcules
Total (without water)40,2062
Polymers40,2062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-8 kcal/mol
Surface area15800 Å2
MethodPISA
3
B: Serine-aspartate repeat-containing protein E
F: Peptide from Complement factor H


Theoretical massNumber of molelcules
Total (without water)40,2062
Polymers40,2062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-2 kcal/mol
Surface area15540 Å2
MethodPISA
4
C: Serine-aspartate repeat-containing protein E
G: Peptide from Complement factor H


Theoretical massNumber of molelcules
Total (without water)40,2062
Polymers40,2062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-2 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.500, 117.500, 154.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q932F7
#2: Protein/peptide
Peptide from Complement factor H / H factor 1


Mass: 2511.836 Da / Num. of mol.: 4 / Fragment: UNP residues 1206-1226 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08603

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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: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES sodium pH 7.5, 0.2M Magnesium chloride, 30% PEG 400 (v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 3.3→49.79 Å / Num. obs: 31291 / % possible obs: 96.1 % / Redundancy: 2.8 % / Rsym value: 0.1 / Net I/σ(I): 7
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.9 / Num. measured obs: 4613 / Rsym value: 0.56 / % possible all: 97.9

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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: 3.3→49.79 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.886 / Cross valid method: THROUGHOUT / ESU R Free: 0.568 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28097 1580 5.1 %RANDOM
Rwork0.22189 ---
obs0.22483 29695 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 89.516 Å2
Baniso -1Baniso -2Baniso -3
1--3.02 Å20 Å2-0 Å2
2---3.51 Å20 Å2
3---6.52 Å2
Refinement stepCycle: 1 / Resolution: 3.3→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10427 0 0 0 10427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0210589
X-RAY DIFFRACTIONr_bond_other_d00.029770
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.94614360
X-RAY DIFFRACTIONr_angle_other_deg3.726322587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54151315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.59426.525518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.009151843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2351524
X-RAY DIFFRACTIONr_chiral_restr0.0780.21653
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212163
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022297
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_it5.7368.9545305
X-RAY DIFFRACTIONr_mcbond_other5.7348.9545304
X-RAY DIFFRACTIONr_mcangle_it8.79413.4226605
X-RAY DIFFRACTIONr_mcangle_other8.79313.4226606
X-RAY DIFFRACTIONr_scbond_it5.5159.2145284
X-RAY DIFFRACTIONr_scbond_other5.5159.2145285
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.60713.7287756
X-RAY DIFFRACTIONr_long_range_B_refined11.53770.80611770
X-RAY DIFFRACTIONr_long_range_B_other11.53670.80811771
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 124 -
Rwork0.326 2225 -
obs--97.67 %

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