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- PDB-6fls: Pentapeptide repeat family protein from Clostridium botulinum -

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Basic information

Entry
Database: PDB / ID: 6fls
TitlePentapeptide repeat family protein from Clostridium botulinum
ComponentsPentapeptide repeat family protein
KeywordsUNKNOWN FUNCTION / Pentapeptide repeat protein Clostridium botulinum
Function / homologyPentapeptide repeats (8 copies) / Pentapeptide repeats (9 copies) / Pentapeptide repeat / Uncharacterized protein
Function and homology information
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMartinez-Carranza, M. / Stenmark, P.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Cotranslational Folding of a Pentarepeat beta-Helix Protein.
Authors: Notari, L. / Martinez-Carranza, M. / Farias-Rico, J.A. / Stenmark, P. / von Heijne, G.
History
DepositionJan 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pentapeptide repeat family protein
B: Pentapeptide repeat family protein
D: Pentapeptide repeat family protein
C: Pentapeptide repeat family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,86119
Polymers109,4804
Non-polymers1,38115
Water3,117173
1
A: Pentapeptide repeat family protein
B: Pentapeptide repeat family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,75313
Polymers54,7402
Non-polymers1,01311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-26 kcal/mol
Surface area19470 Å2
MethodPISA
2
D: Pentapeptide repeat family protein
C: Pentapeptide repeat family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1086
Polymers54,7402
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-23 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.751, 108.475, 112.890
Angle α, β, γ (deg.)90.000, 94.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pentapeptide repeat family protein


Mass: 27369.889 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ACP52_06880 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M0A2X5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 5.8 Å3/Da / Density % sol: 78.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.8→112.53 Å / Num. obs: 63384 / % possible obs: 99.2 % / Redundancy: 3.8 % / Net I/σ(I): 10.1
Reflection shellResolution: 2.8→2.87 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→112.53 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3079 4.9 %RANDOM
Rwork0.1699 ---
obs0.1716 60286 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 149 Å2 / Biso mean: 59.071 Å2 / Biso min: 28 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å21.42 Å2
2---1.88 Å20 Å2
3---0.39 Å2
Refinement stepCycle: final / Resolution: 2.8→112.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6941 0 90 173 7204
Biso mean--87.02 51.04 -
Num. residues----865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0157172
X-RAY DIFFRACTIONr_bond_other_d0.0010.0186380
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.7439655
X-RAY DIFFRACTIONr_angle_other_deg3.71.75714929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8565861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91623.657309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.691151118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2041516
X-RAY DIFFRACTIONr_chiral_restr0.060.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027911
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021461
X-RAY DIFFRACTIONr_mcbond_it3.6225.7153456
X-RAY DIFFRACTIONr_mcbond_other3.6215.7163457
X-RAY DIFFRACTIONr_mcangle_it5.4838.5684313
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 185 -
Rwork0.351 4458 -
all-4643 -
obs--99.19 %

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