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- PDB-8wen: Bacteroides fragilis toxin 2 -

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Basic information

Entry
Database: PDB / ID: 8wen
TitleBacteroides fragilis toxin 2
ComponentsMetalloprotease
KeywordsTOXIN / Bacteroides fragilis / BFT1 / metalloenzyme
Function / homology
Function and homology information


metallopeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Fragilysin / Fragilysin, N-terminal / Fragilysin, N-terminal domain superfamily / N-terminal domain of fragilysin / Metallo-peptidase family M12 / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsGuo, Y. / Wen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Bacteroides fragilis toxin 2
Authors: Guo, Y. / Wen, Y.
History
DepositionSep 18, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Metalloprotease
A: Metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2365
Polymers89,0822
Non-polymers1543
Water7,963442
1
C: Metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6062
Polymers44,5411
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area14590 Å2
MethodPISA
2
A: Metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6293
Polymers44,5411
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-40 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.354, 99.579, 114.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Metalloprotease


Mass: 44541.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: bft-2 / Production host: Escherichia coli (E. coli) / References: UniProt: O05091
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.8 Å3/Da / Density % sol: 56.08 %
Crystal growTemperature: 193 K / Method: vapor diffusion, sitting drop
Details: 4% v/v Tacsimate pH 5.0, 12% w/v Polyethylene glycol 3350, 32 mg mL-1.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.97→43.26 Å / Num. obs: 135806 / % possible obs: 99.5 % / Redundancy: 12.8 % / CC1/2: 0.999 / Net I/σ(I): 14.76
Reflection shellResolution: 1.97→2.041 Å / Num. unique obs: 6653 / CC1/2: 0.626

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→43.26 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 3810 2.81 %
Rwork0.1803 --
obs0.1811 135806 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→43.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5302 0 3 442 5747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065450
X-RAY DIFFRACTIONf_angle_d0.8237375
X-RAY DIFFRACTIONf_dihedral_angle_d15.986734
X-RAY DIFFRACTIONf_chiral_restr0.05805
X-RAY DIFFRACTIONf_plane_restr0.005951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-20.51951250.39484274X-RAY DIFFRACTION87
2-2.020.30791420.30684875X-RAY DIFFRACTION100
2.02-2.050.31211460.28484967X-RAY DIFFRACTION100
2.05-2.080.30921440.26724901X-RAY DIFFRACTION100
2.08-2.110.29581390.26144921X-RAY DIFFRACTION100
2.11-2.140.25821410.2364889X-RAY DIFFRACTION100
2.14-2.180.29261390.22894932X-RAY DIFFRACTION100
2.18-2.220.2621440.23364919X-RAY DIFFRACTION100
2.22-2.260.24921400.23024910X-RAY DIFFRACTION100
2.26-2.30.23451440.21484905X-RAY DIFFRACTION100
2.3-2.350.24841450.20614885X-RAY DIFFRACTION100
2.35-2.40.25481430.20394905X-RAY DIFFRACTION100
2.4-2.450.2881450.20324956X-RAY DIFFRACTION100
2.45-2.510.26071410.19274849X-RAY DIFFRACTION100
2.51-2.580.19551420.19594964X-RAY DIFFRACTION100
2.58-2.660.2231440.19014902X-RAY DIFFRACTION100
2.66-2.740.19451420.18234884X-RAY DIFFRACTION100
2.74-2.840.23311400.18374918X-RAY DIFFRACTION100
2.84-2.960.23181380.19384948X-RAY DIFFRACTION100
2.96-3.090.20371440.18934900X-RAY DIFFRACTION100
3.09-3.250.21741430.18914911X-RAY DIFFRACTION100
3.25-3.460.20031440.18044923X-RAY DIFFRACTION100
3.46-3.720.1941470.16164905X-RAY DIFFRACTION100
3.72-4.10.17471430.15124923X-RAY DIFFRACTION100
4.1-4.690.15691350.13354875X-RAY DIFFRACTION100
4.69-5.910.21021370.15074938X-RAY DIFFRACTION100
5.91-43.260.15571330.16454917X-RAY DIFFRACTION100

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