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- PDB-3asw: Structural and biochemical characterization of ClfB:ligand intera... -

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Basic information

Entry
Database: PDB / ID: 3asw
TitleStructural and biochemical characterization of ClfB:ligand interactions
Components
  • Clumping factor B
  • Tail region derived peptide
KeywordsCELL ADHESION / IgG like / Adhesin / Cytokeratin
Function / homology
Function and homology information


positive regulation of epidermis development / structural constituent of skin epidermis / keratin filament / Keratinization / intermediate filament organization / Formation of the cornified envelope / peptide cross-linking / cornified envelope / protein heterotetramerization / intermediate filament ...positive regulation of epidermis development / structural constituent of skin epidermis / keratin filament / Keratinization / intermediate filament organization / Formation of the cornified envelope / peptide cross-linking / cornified envelope / protein heterotetramerization / intermediate filament / epidermis development / keratinocyte differentiation / epithelial cell differentiation / cytoskeleton / cell adhesion / protein heterodimerization activity / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Keratin, type I / 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 / Intermediate filament protein, conserved site / Intermediate filament protein ...Keratin, type I / 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 / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Keratin, type I cytoskeletal 10 / Clumping factor B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGanesh, V.K.
CitationJournal: To be published
Title: Structural and biochemical characterization of ClfB:ligand interactions
Authors: Ganesh, V.K. / Barbu, E.M. / Deivanayagam, C.C.S. / Le, B. / Anderson, A. / Matsuka, Y. / Lin, S.L. / Foster, T.J. / Narayana, SV.L. / Hook, M.
History
DepositionDec 22, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clumping factor B
B: Tail region derived peptide


Theoretical massNumber of molelcules
Total (without water)37,8522
Polymers37,8522
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-3 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.598, 85.598, 84.795
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Clumping factor B / Fibrinogen receptor B / Fibrinogen-binding protein B


Mass: 36671.164 Da / Num. of mol.: 1 / Fragment: N2 N3 domain (UNP RESIDUES 212-531) / Mutation: D444E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: clfB, SA2423 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A382
#2: Protein/peptide Tail region derived peptide / 15-mer from Keratin / type I cytoskeletal 10


Mass: 1181.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Homo sapiens (human) / References: UniProt: P13645
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 4.1 Å3/Da / Density % sol: 70.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 0.9M sodium citrate, 90mM imidazole pH 8.0 , VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 18830

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.087 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 973 5.2 %RANDOM
Rwork0.1817 ---
obs0.1836 18813 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.25 Å2 / Biso mean: 38.2061 Å2 / Biso min: 17.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2519 0 0 134 2653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222569
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.9283495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4295329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09526.048124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27215392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.697155
X-RAY DIFFRACTIONr_chiral_restr0.1070.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022000
X-RAY DIFFRACTIONr_nbd_refined0.2310.21105
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21772
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2142
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0630.23
X-RAY DIFFRACTIONr_mcbond_it1.95631663
X-RAY DIFFRACTIONr_mcangle_it2.90432633
X-RAY DIFFRACTIONr_scbond_it2.2231026
X-RAY DIFFRACTIONr_scangle_it3.1133862
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 87 -
Rwork0.299 1274 -
all-1361 -
obs--99.49 %

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