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- PDB-4f1z: Crystal structures reveal the multi-ligand binding mechanism of t... -

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Basic information

Entry
Database: PDB / ID: 4f1z
TitleCrystal structures reveal the multi-ligand binding mechanism of the Staphylococcus aureus ClfB
Components
  • Clumping factor B
  • peptide from Keratin, type I cytoskeletal 10
KeywordsCELL ADHESION / Dev-IgG fold / protein-peptide complex / CK10 / Cell Surface
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYang, M.J. / Xiang, H. / Wang, J.W. / Liu, B. / Chen, Y.G. / Liu, L. / Deng, X.M. / Feng, Y.
CitationJournal: Plos Pathog. / Year: 2012
Title: Crystal Structures Reveal the Multi-Ligand Binding Mechanism of Staphylococcus aureus ClfB
Authors: Xiang, H. / Feng, Y. / Wang, J.W. / Liu, B. / Chen, Y.G. / Liu, L. / Deng, X.M. / Yang, M.J.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Clumping factor B
Q: peptide from Keratin, type I cytoskeletal 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9433
Polymers40,9182
Non-polymers241
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-14 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.331, 70.331, 177.157
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 39875.512 Da / Num. of mol.: 1 / Fragment: N2 N3 domain, UNP residues 197-542
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: clfB, SAR2709 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6GDH2
#2: Protein/peptide peptide from Keratin, type I cytoskeletal 10 / Cytokeratin-10 / CK-10 / Keratin-10 / K10


Mass: 1042.966 Da / Num. of mol.: 1 / Fragment: tail region, UNP residues 473-486 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: P13645
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate tribasic dehydrate, 20% 2-propanol, 20% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.055→50.188 Å / Num. all: 18865 / Num. obs: 18865 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 33.95 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.0552-2.163515
2.1635-2.2991114
2.2991-2.4766131
2.4766-2.7258165
2.7258-3.1202193
3.1202-3.9309197

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F27

4f27


Resolution: 2.3→50.188 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.718 / SU ML: 0.28 / σ(F): 0.04 / Phase error: 32.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 938 5.02 %RANDOM
Rwork0.2475 ---
obs0.2477 18865 77.61 %-
all-18865 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.779 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso max: 194.75 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-17.7334 Å2-0 Å2-0 Å2
2--17.7334 Å20 Å2
3----36.064 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 1 11 2594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082630
X-RAY DIFFRACTIONf_angle_d1.1673563
X-RAY DIFFRACTIONf_chiral_restr0.074390
X-RAY DIFFRACTIONf_plane_restr0.005471
X-RAY DIFFRACTIONf_dihedral_angle_d16.254946
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3002-2.42150.5046360.346689292828
2.4215-2.57320.3008730.33541425149846
2.5732-2.77180.33421400.34832485262580
2.7718-3.05070.33451670.32622943311094
3.0507-3.49210.32031670.27953038320597
3.4921-4.39930.21091750.22143148332398
4.3993-50.20020.19471520.19963282343497
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.77920.28380.12150.3110.62563.45540.6415-0.534-0.14370.3485-0.46560.0149-0.97841.69190.25721.1218-1.0798-0.27621.65270.2280.523836.8857-13.886726.3598
21.50410.1645-0.42621.020.05035.78910.2971-0.7536-0.3012-0.0892-0.69040.1673-0.274-0.0480.16270.4486-0.2679-0.03220.63110.00630.374721.405-19.0217.1699
30.30590.1378-0.79180.7903-0.8853.76580.0233-0.5423-0.41930.2298-0.5249-0.1392-0.49381.13850.1091-0.0358-0.954-0.07050.95320.28840.410531.8737-23.005422.0407
40.72770.4235-0.08450.80860.1394.4276-0.2832-0.1338-0.4248-0.2144-0.1725-0.27690.13221.74180.37480.3172-0.6067-0.05841.81790.34340.430740.7623-22.690922.3108
50.36390.7331-0.40441.38840.05814.76220.1334-0.2876-0.1618-0.5049-0.50690.2813-1.3996-0.631-0.04210.3411-0.39340.01760.6975-0.05720.294915.9516-20.778212.1122
63.77120.87941.93740.9687-0.97285.2634-0.0227-0.43290.03060.4628-0.61410.07910.5740.0390.3340.7995-0.33880.00970.890.20060.525122.1207-40.862715.6392
70.89350.35310.11391.01830.75074.09970.2522-0.26960.26830.2666-0.6860.26150.8425-1.5920.35870.5695-0.69750.04311.1171-0.16290.42953.1513-40.947410.561
81.64540.6025-0.31681.72650.04214.54470.1298-0.01720.0390.2115-0.649-0.23071.5282-0.16270.25020.8762-0.26940.04790.92390.16640.536620.1314-43.65589.0562
91.21340.10.73550.79320.26865.43390.1161-0.50730.66620.3244-0.50630.47620.5395-2.0320.58180.6291-0.66540.10061.4076-0.30690.6466-2.4167-40.5458-1.6564
100.02580.1079-0.02210.47050.2584.54280.3112-0.22950.2319-0.3453-0.4278-0.39070.31180.34920.39490.4655-0.27680.02160.67030.01760.527424.2376-31.09885.9773
110.0776-0.1275-0.05780.24610.05510.05360.13130.2450.0058-0.1309-0.2949-0.13310.13730.0838-0.00090.4517-0.37450.07430.9547-0.03110.53817.9652-32.16414.6542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 210:224)
2X-RAY DIFFRACTION2(chain A and resid 225:241)
3X-RAY DIFFRACTION3(chain A and resid 242:285)
4X-RAY DIFFRACTION4(chain A and resid 286:318)
5X-RAY DIFFRACTION5(chain A and resid 319:379)
6X-RAY DIFFRACTION6(chain A and resid 380:391)
7X-RAY DIFFRACTION7(chain A and resid 392:487)
8X-RAY DIFFRACTION8(chain A and resid 488:501)
9X-RAY DIFFRACTION9(chain A and resid 502:523)
10X-RAY DIFFRACTION10(chain A and resid 524:531)
11X-RAY DIFFRACTION11(chain Q and resid 8:21)

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