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- PDB-7c7r: Biofilm associated protein - B domain -

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Basic information

Entry
Database: PDB / ID: 7c7r
TitleBiofilm associated protein - B domain
ComponentsBiofilm-associated surface protein
KeywordsCELL ADHESION / Cell wall-anchored surface protein / biofilm formation
Function / homology
Function and homology information


cell-abiotic substrate adhesion / single-species submerged biofilm formation / cell-cell adhesion / extracellular region / metal ion binding / membrane
Similarity search - Function
Bacterial Ig domain / Bacterial Ig domain / 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
Similarity search - Domain/homology
Biofilm-associated surface protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.07 Å
AuthorsMa, J.F. / Xu, Z.H. / Zhang, Y.K. / Cheng, X. / Fan, S.L. / Wang, J.W. / Fang, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31872712 China
Citation
Journal: Embo J. / Year: 2021
Title: Structural mechanism for modulation of functional amyloid and biofilm formation by Staphylococcal Bap protein switch.
Authors: Ma, J. / Cheng, X. / Xu, Z. / Zhang, Y. / Valle, J. / Fan, S. / Zuo, X. / Lasa, I. / Fang, X.
#1: Journal: To Be Published
Title: Integrative structure and functional implications of a 236-kDa modular protein Bap from Staphylococcus aureus
Authors: Ma, J.F. / Zhang, Y.K. / Cheng, X. / Fan, S.L. / Xu, N. / Fang, X.Y.
History
DepositionMay 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Author supporting evidence / Database references / Structure summary
Category: citation_author / pdbx_audit_support / struct_keywords
Item: _pdbx_audit_support.grant_number / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Jun 2, 2021Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Jul 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.5May 29, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Biofilm-associated surface protein
A: Biofilm-associated surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,93512
Polymers99,5352
Non-polymers40110
Water54030
1
B: Biofilm-associated surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9686
Polymers49,7671
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-12 kcal/mol
Surface area18040 Å2
MethodPISA
2
A: Biofilm-associated surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9686
Polymers49,7671
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.171, 171.171, 102.503
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))
21(chain B and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASNASN(chain A and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))AB361 - 54727 - 213
12ALAALALYSLYS(chain A and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))AB549 - 775215 - 441
13CACACACA(chain A and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))AH - L801 - 805
21GLNGLNASNASN(chain B and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))BA361 - 54727 - 213
22ALAALALYSLYS(chain B and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))BA549 - 775215 - 441
23CACACACA(chain B and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))BC - G801 - 805

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Components

#1: Protein Biofilm-associated surface protein


Mass: 49767.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: bap / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): B834 / References: UniProt: Q79LN3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.06 Å3/Da / Density % sol: 69.67 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium Cacodylate pH 6.5, 40% MPD, 5% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 3.07→49.1 Å / Num. obs: 27970 / % possible obs: 96.42 % / Redundancy: 2 % / Biso Wilson estimate: 76.02 Å2 / CC1/2: 0.999 / Net I/σ(I): 25.33
Reflection shellResolution: 3.07→3.18 Å / Num. unique obs: 2317 / CC1/2: 0.661

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
STARANISOdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.07→49.1 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 1399 5 %
Rwork0.1918 26569 -
obs0.1935 27968 96.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.71 Å2 / Biso mean: 71.6052 Å2 / Biso min: 25.82 Å2
Refinement stepCycle: final / Resolution: 3.07→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6480 0 10 30 6520
Biso mean--68.17 55.01 -
Num. residues----830
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2492X-RAY DIFFRACTION4.314TORSIONAL
12B2492X-RAY DIFFRACTION4.314TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.07-3.180.33541160.2882200231682
3.18-3.310.29491230.27052354247787
3.31-3.460.27431370.22222582271996
3.46-3.640.261430.209427142857100
3.64-3.870.25851430.188827282871100
3.87-4.170.21671440.179827352879100
4.17-4.580.17591450.144327392884100
4.59-5.250.15721450.148227702915100
5.25-6.610.22661480.205628022950100
6.61-49.850.23081550.204329453100100
Refinement TLS params.Method: refined / Origin x: 139.4015 Å / Origin y: 62.7425 Å / Origin z: 24.636 Å
111213212223313233
T0.2948 Å2-0.0356 Å20.0557 Å2-0.3623 Å2-0.0108 Å2--0.2829 Å2
L0.6057 °20.2265 °20.0894 °2-0.8434 °2-0.1489 °2--0.48 °2
S0.0103 Å °0.0148 Å °0.0587 Å °0.0856 Å °0.0364 Å °0.0781 Å °-0.14 Å °0.0452 Å °-0.0009 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB361 - 775
2X-RAY DIFFRACTION1allB801 - 910
3X-RAY DIFFRACTION1allA361 - 775
4X-RAY DIFFRACTION1allA801 - 922

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