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- PDB-8wem: Bacteroides fragilis toxin 1 -

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Basic information

Entry
Database: PDB / ID: 8wem
TitleBacteroides fragilis toxin 1
ComponentsFragilysin
KeywordsTOXIN / Bacteroides fragilis / BFT1 / metalloenzyme
Function / homology
Function and homology information


fragilysin / metallopeptidase activity / toxin activity / proteolysis / extracellular region / 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 / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1
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: Fragilysin
A: Fragilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0314
Polymers88,9002
Non-polymers1312
Water9,944552
1
C: Fragilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5152
Polymers44,4501
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fragilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5152
Polymers44,4501
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.672, 82.672, 280.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Fragilysin / Enterotoxin


Mass: 44449.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: btfP / Production host: Escherichia coli (E. coli) / References: UniProt: P54355, fragilysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium malonate pH 5.0, 20% 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: BL18U1 / 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: 1.8→46.37 Å / Num. obs: 171231 / % possible obs: 99.87 % / Redundancy: 20.6 % / Biso Wilson estimate: 33.17 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.18
Reflection shellResolution: 1.8→1.866 Å / Num. unique obs: 8887 / CC1/2: 0.727

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.37 Å / SU ML: 0.2234 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.3134
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2023 3757 2.19 %
Rwork0.1759 167474 -
obs0.1764 171231 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.34 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5511 0 2 552 6065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00765675
X-RAY DIFFRACTIONf_angle_d0.87177693
X-RAY DIFFRACTIONf_chiral_restr0.0584843
X-RAY DIFFRACTIONf_plane_restr0.0059996
X-RAY DIFFRACTIONf_dihedral_angle_d6.1239769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.42081390.42096135X-RAY DIFFRACTION99.56
1.82-1.850.31681380.34286198X-RAY DIFFRACTION99.72
1.85-1.870.33751390.31956213X-RAY DIFFRACTION99.75
1.87-1.90.30831350.30166163X-RAY DIFFRACTION99.7
1.9-1.930.29891380.30266247X-RAY DIFFRACTION99.81
1.93-1.960.31881410.29026215X-RAY DIFFRACTION99.84
1.96-1.990.26471390.2476135X-RAY DIFFRACTION99.76
1.99-2.030.24531440.22886251X-RAY DIFFRACTION99.77
2.03-2.060.19081400.20716173X-RAY DIFFRACTION99.75
2.06-2.10.26431380.20086188X-RAY DIFFRACTION99.72
2.1-2.140.1941390.19226163X-RAY DIFFRACTION99.83
2.14-2.190.23641370.1826232X-RAY DIFFRACTION99.84
2.19-2.240.21431410.19366231X-RAY DIFFRACTION99.95
2.24-2.30.24451360.18516214X-RAY DIFFRACTION99.94
2.3-2.360.19931420.17786210X-RAY DIFFRACTION100
2.36-2.430.23561390.18456224X-RAY DIFFRACTION100
2.43-2.510.24881360.18456194X-RAY DIFFRACTION99.94
2.51-2.60.22261380.18616195X-RAY DIFFRACTION100
2.6-2.70.21411380.18186189X-RAY DIFFRACTION100
2.7-2.820.23361340.1846234X-RAY DIFFRACTION100
2.82-2.970.20061420.18646224X-RAY DIFFRACTION100
2.97-3.160.18811400.17886209X-RAY DIFFRACTION99.97
3.16-3.40.19171410.16556174X-RAY DIFFRACTION100
3.4-3.750.19451370.15616248X-RAY DIFFRACTION100
3.75-4.290.17291370.13796197X-RAY DIFFRACTION100
4.29-5.40.1421440.12996211X-RAY DIFFRACTION100
5.4-46.370.18591450.15826207X-RAY DIFFRACTION99.91
Refinement TLS params.Method: refined / Origin x: -23.4409588652 Å / Origin y: 37.9607951437 Å / Origin z: -32.0879588843 Å
111213212223313233
T0.307772583143 Å20.0107879805905 Å2-0.00816306057491 Å2-0.243700858465 Å20.00311409514547 Å2--0.300839761196 Å2
L0.541957395138 °20.195085836059 °2-0.428681175375 °2-0.35252917586 °2-0.303781093452 °2--1.01109072348 °2
S0.0362531447678 Å °-0.00139552621721 Å °-0.00174331841189 Å °-0.0384637152247 Å °-0.0110187473326 Å °0.00658786165113 Å °-0.0708592709083 Å °-0.0404053152669 Å °-0.000921518218311 Å °
Refinement TLS groupSelection details: all

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