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- PDB-7c7u: Biofilm associated protein - BSP domain -

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Basic information

Entry
Database: PDB / ID: 7c7u
TitleBiofilm associated protein - BSP 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.93 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 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 1.3Jul 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Nov 29, 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: Biofilm-associated surface protein
B: Biofilm-associated surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,58512
Polymers131,1842
Non-polymers40110
Water23,8341323
1
A: Biofilm-associated surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7936
Polymers65,5921
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-12 kcal/mol
Surface area26160 Å2
MethodPISA
2
B: Biofilm-associated surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7936
Polymers65,5921
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-12 kcal/mol
Surface area26100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.737, 167.726, 89.316
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND (RESID 354 THROUGH 402 OR RESID 407...
21CHAIN B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(CHAIN A AND (RESID 354 THROUGH 402 OR RESID 407...A354
121(CHAIN A AND (RESID 354 THROUGH 402 OR RESID 407...A407
131(CHAIN A AND (RESID 354 THROUGH 402 OR RESID 407...A472
141(CHAIN A AND (RESID 354 THROUGH 402 OR RESID 407...A623
151(CHAIN A AND (RESID 354 THROUGH 402 OR RESID 407...A914
161(CHAIN A AND (RESID 354 THROUGH 402 OR RESID 407...A948
211CHAIN BB354 - 947

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Components

#1: Protein Biofilm-associated surface protein


Mass: 65592.117 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 / Water


Mass: 18.015 Da / Num. of mol.: 1323 / 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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium Citrate pH5.0, 10% 2-propanol, 26% PEG400

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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: 1.93→49.44 Å / Num. obs: 111309 / % possible obs: 97.76 % / Redundancy: 4.7 % / CC1/2: 0.999 / Net I/σ(I): 16.71
Reflection shellResolution: 1.93→2 Å / Num. unique obs: 9729 / CC1/2: 0.819

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
MOLREPphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C7R

7c7r


Resolution: 1.93→49.44 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 5563 5 %
Rwork0.208 105675 -
obs0.21 111238 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.5 Å2 / Biso mean: 43.65 Å2 / Biso min: 18.59 Å2
Refinement stepCycle: final / Resolution: 1.93→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8792 0 10 1323 10125
Biso mean--37.45 49.63 -
Num. residues----1156
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5408X-RAY DIFFRACTIONPOSITIONAL0
12B5408X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.93-1.950.33941450.34242748289377
1.95-1.980.38461640.3073112327687
1.98-20.35181780.29333371354993
2-2.020.34171850.27393526371198
2.02-2.050.32691870.25343542372999
2.05-2.080.29571880.25853597378599
2.08-2.110.33091850.25123494367999
2.11-2.140.3081890.23953587377699
2.14-2.170.29461860.23313543372999
2.17-2.210.2831880.22913573376199
2.21-2.250.27781890.22293589377899
2.25-2.290.28231880.22323559374799
2.29-2.330.26961860.2213531371799
2.33-2.380.27741880.22053569375799
2.38-2.430.29491880.22083581376999
2.43-2.490.27151890.21753586377599
2.49-2.550.29181880.21833568375699
2.55-2.620.29651880.224935803768100
2.62-2.70.28911900.232536023792100
2.7-2.780.27431890.22293588377799
2.78-2.880.29241890.22393588377799
2.88-30.24391870.20813547373499
3-3.140.26781890.216536023791100
3.14-3.30.26451880.207935773765100
3.3-3.510.22431900.181236023792100
3.51-3.780.22321850.18113515370098
3.78-4.160.23351900.181136143804100
4.16-4.760.21261910.17436173808100
4.76-5.990.23061860.19453557374398
6-49.440.22221900.21523610380098

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