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- PDB-8jl8: Crystal structure of the collagen binding domain of Cnm from Stre... -

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Basic information

Entry
Database: PDB / ID: 8jl8
TitleCrystal structure of the collagen binding domain of Cnm from Streptococcus mutans
ComponentsCollagen-binding adhesin
KeywordsPROTEIN BINDING / Streptococcus mutans / Collagen binding domain
Function / homology
Function and homology information


collagen binding / cell adhesion / extracellular region
Similarity search - Function
Collagen binding domain / Collagen binding domain / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Collagen-binding adhesin
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsTanaka, S.-i. / Hirata, A. / Takano, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15K15749 Japan
Japan Society for the Promotion of Science (JSPS)18K09735 Japan
Japan Society for the Promotion of Science (JSPS)22K10233 Japan
CitationJournal: Chemistry / Year: 2023
Title: Structure, Stability and Binding Properties of Collagen-Binding Domains from Streptococcus mutans.
Authors: Nishi, A. / Matsui, H. / Hirata, A. / Mukaiyama, A. / Tanaka, S.-i. / Yoshizawa, T. / Matsumura, H. / Nomura, R. / Nakano, K. / Takano, K.
History
DepositionJun 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen-binding adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,71212
Polymers34,6711
Non-polymers1,04111
Water1,982110
1
A: Collagen-binding adhesin
hetero molecules

A: Collagen-binding adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,42524
Polymers69,3432
Non-polymers2,08222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2420 Å2
ΔGint-103 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.915, 40.915, 364.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Collagen-binding adhesin


Mass: 34671.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: cnm / Plasmid: pET42a / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B9A878
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22% (w/v) PEG 6000, 100 mM Ammonium sulfate and 10% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 28413 / % possible obs: 99.4 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 27.2
Reflection shellResolution: 1.81→1.84 Å / Num. unique obs: 2689 / CC1/2: 0.736

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→45.65 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.945 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24631 1476 4.9 %RANDOM
Rwork0.22205 ---
obs0.22331 28413 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.867 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å2-0 Å2
2--0.36 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 1.81→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 59 110 2405
LS refinement shellResolution: 1.813→1.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 92 -
Rwork0.324 2082 -
obs--99.5 %

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