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- PDB-6ekt: Structure of P47 from Clostridium botulinum A2 -

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Basic information

Entry
Database: PDB / ID: 6ekt
TitleStructure of P47 from Clostridium botulinum A2
Componentsp-47 protein
KeywordsLIPID BINDING PROTEIN / lipid binding
Function / homologyClostridium P47 protein / Clostridium P-47 protein / p-47 protein
Function and homology information
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsBerntsson, R.P. / Stenmark, P.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2016-03599 Sweden
European Molecular Biology OrganizationGA-2010- 267146 Sweden
CitationJournal: FEBS Lett. / Year: 2017
Title: Crystal structures of OrfX2 and P47 from a Botulinum neurotoxin OrfX-type gene cluster.
Authors: Gustafsson, R. / Berntsson, R.P. / Martinez-Carranza, M. / El Tekle, G. / Odegrip, R. / Johnson, E.A. / Stenmark, P.
History
DepositionSep 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 6, 2017Group: Database references / Structure summary / Category: audit_author / citation
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4May 8, 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)50,0741
Polymers50,0741
Non-polymers00
Water5,368298
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.470, 38.927, 82.761
Angle α, β, γ (deg.)90.000, 107.950, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein p-47 protein


Mass: 50073.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (strain Kyoto / Type A2) (bacteria)
Strain: Kyoto / Type A2 / Gene: p47, CLM_0895 / Production host: Escherichia coli (E. coli) / References: UniProt: C1FUH7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.2 M Ammonium Acetate, 0.1 M BisTris, 22-31% PEG3000 (+/- 10 mM BaCl2)
PH range: 4.9-5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.75→39.37 Å / Num. obs: 46996 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 2.716 % / Biso Wilson estimate: 34.349 Å2 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.05 / Χ2: 0.923 / Net I/σ(I): 16.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
1.75-1.852.6820.91.5274201.11597.1
1.85-1.982.7320.439371250.54199.4
1.98-2.142.7280.215.9266850.2699.3
2.14-2.342.7410.1279.1161030.15799.2
2.34-2.622.740.07114.455520.08999
2.62-3.022.7310.03924.1548990.04998.5
3.02-3.692.7180.02240.2741280.02797.9
3.69-5.22.6890.01554.5232330.01897.6
5.2-39.372.60.01257.7518510.01695.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→39.37 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.86 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.122
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 2350 5 %RANDOM
Rwork0.1979 ---
obs0.1998 44643 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.44 Å2 / Biso mean: 35.238 Å2 / Biso min: 18.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å21.08 Å2
2---0.23 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 1.75→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 0 298 3675
Biso mean---40.54 -
Num. residues----419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023477
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9444708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.44525.774168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04115627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.446158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022612
LS refinement shellResolution: 1.748→1.793 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 164 -
Rwork0.341 3121 -
all-3285 -
obs--94.32 %
Refinement TLS params.Method: refined / Origin x: -7.0728 Å / Origin y: -16.1854 Å / Origin z: 18.6902 Å
111213212223313233
T0.0398 Å2-0.0564 Å20.0143 Å2-0.1037 Å2-0.0226 Å2--0.0082 Å2
L2.2658 °20.2513 °2-1.5707 °2-0.1184 °2-0.185 °2--1.2324 °2
S0.1433 Å °-0.3556 Å °0.1136 Å °0.0152 Å °-0.0456 Å °0.0103 Å °-0.1533 Å °0.2844 Å °-0.0977 Å °

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