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- PDB-7dm0: Biofilm associated protein - C region -

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Basic information

Entry
Database: PDB / ID: 7dm0
TitleBiofilm associated protein - C region
ComponentsBiofilm-associated surface protein
KeywordsCELL ADHESION / Biofilm
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 / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMa, J.F. / Fang, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)3187040085 China
CitationJournal: To Be Published
Title: Biofilm associated protein - C region
Authors: Ma, J.F. / Fang, X.Y.
History
DepositionDec 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)40,4584
Polymers40,3782
Non-polymers802
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-29 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.354, 45.899, 74.391
Angle α, β, γ (deg.)90.000, 91.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain DA0
211chain FB0

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Components

#1: Protein Biofilm-associated surface protein


Mass: 20189.068 Da / Num. of mol.: 2 / Fragment: UNP residues 1908-2146
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) / References: UniProt: Q79LN3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.09 Å3/Da / Density % sol: 41.02 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris hydrochloride pH8.5, 0.1M Magnesium chloride, 20% PEG400, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.55→41.75 Å / Num. obs: 47661 / % possible obs: 97.79 % / Redundancy: 4.1 % / CC1/2: 0.997 / Net I/σ(I): 12.43
Reflection shellResolution: 1.55→1.605 Å / Num. unique obs: 4084 / CC1/2: 0.709

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M3A

6m3a


Resolution: 1.55→41.75 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 2381 5 %
Rwork0.1978 45280 -
obs0.199 47661 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.04 Å2 / Biso mean: 27.5643 Å2 / Biso min: 13.95 Å2
Refinement stepCycle: final / Resolution: 1.55→41.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 2 363 2751
Biso mean--17.97 37.73 -
Num. residues----334
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1002X-RAY DIFFRACTION1.103TORSIONAL
12B1002X-RAY DIFFRACTION1.103TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.580.42531060.38982099220578
1.58-1.610.3331270.30632422254989
1.61-1.650.29181410.26062687282897
1.65-1.690.27091420.228226762818100
1.69-1.740.27821410.2192680282199
1.74-1.790.23871430.203626822825100
1.79-1.850.24371420.202427202862100
1.85-1.910.23431430.188227342877100
1.91-1.990.20131420.18372693283599
1.99-2.080.20181420.18462693283599
2.08-2.190.21591430.17852722286599
2.19-2.330.23771450.19192718286399
2.33-2.510.19181420.195427012843100
2.51-2.760.2161430.20382729287299
2.76-3.160.21581440.197727222866100
3.16-3.980.20231460.175927742920100
3.98-41.750.21591490.201228282977100

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