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- PDB-5wix: Crystal structure of P47 of Clostridium botulinum E1 -

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Basic information

Entry
Database: PDB / ID: 5wix
TitleCrystal structure of P47 of Clostridium botulinum E1
Componentsp-47 protein
KeywordsUNKNOWN FUNCTION / BPI-like / Tulip domain fold / hypothetical protein
Function / homologyClostridium P47 protein / Clostridium P-47 protein / p-47 protein
Function and homology information
Biological speciesClostridium botulinum E1 str. 'BoNT E Beluga' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsLam, K. / Liu, S. / Qi, R. / Jin, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI091823 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI125704 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI123920 United States
CitationJournal: Toxicon / Year: 2018
Title: The hypothetical protein P47 of Clostridium botulinum E1 strain Beluga has a structural topology similar to bactericidal/permeability-increasing protein.
Authors: Lam, K.H. / Qi, R. / Liu, S. / Kroh, A. / Yao, G. / Perry, K. / Rummel, A. / Jin, R.
History
DepositionJul 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: p-47 protein


Theoretical massNumber of molelcules
Total (without water)51,0031
Polymers51,0031
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.080, 74.080, 308.180
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 p-47 protein


Mass: 51002.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum E1 str. 'BoNT E Beluga' (bacteria)
Gene: p47, CLO_2650 / Production host: Escherichia coli (E. coli) / References: UniProt: C5UY13

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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: 4.14 Å3/Da / Density % sol: 70.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 12 % PEG 6000, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.8→43.32 Å / Num. obs: 22009 / % possible obs: 99.08 % / Redundancy: 5.5 % / Rpim(I) all: 0.072 / Net I/σ(I): 12.48
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.6 / Rpim(I) all: 0.703 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata scaling
AutoSolphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.8→43.319 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 1061 4.84 %
Rwork0.2286 --
obs0.231 21917 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→43.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 0 0 3242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093307
X-RAY DIFFRACTIONf_angle_d1.2464481
X-RAY DIFFRACTIONf_dihedral_angle_d14.7111187
X-RAY DIFFRACTIONf_chiral_restr0.052513
X-RAY DIFFRACTIONf_plane_restr0.005566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.92750.42571230.37562554X-RAY DIFFRACTION99
2.9275-3.08180.3751290.33512585X-RAY DIFFRACTION99
3.0818-3.27480.38751240.32182555X-RAY DIFFRACTION99
3.2748-3.52760.37011180.26962609X-RAY DIFFRACTION100
3.5276-3.88240.29611260.22682611X-RAY DIFFRACTION100
3.8824-4.44370.23581380.20672601X-RAY DIFFRACTION99
4.4437-5.59660.21531510.17982642X-RAY DIFFRACTION99
5.5966-43.32370.26461520.21112699X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.11860.5755-2.37632.7066-2.48764.2490.51380.27870.48260.13320.00410.2071-1.1562-0.1598-0.53490.82390.16870.18041.42980.3060.830226.350235.5967-50.3899
21.83031.0759-1.1482.3938-2.62317.6822-0.0330.62920.0124-0.1831-0.0092-0.22540.67330.57140.06770.42290.23540.03550.8736-0.06850.574320.41779.7452-15.5529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 169 )
2X-RAY DIFFRACTION2chain 'A' and (resid 170 through 416 )

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