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- PDB-5xcb: X-ray structure of domains D1 and D2 of Clostridium perfringens p... -

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Basic information

Entry
Database: PDB / ID: 5xcb
TitleX-ray structure of domains D1 and D2 of Clostridium perfringens pili protein CppA
ComponentsProbable surface protein
KeywordsSTRUCTURAL PROTEIN / pili protein
Function / homologyGram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Fimbrial isopeptide formation D2 domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold / membrane / Probable surface protein
Function and homology information
Biological speciesClostridium perfringens str. 13 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsKamitori, S. / Tamai, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS KAKENHIJP15K06973, JP15K08482 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structures of major pilins in Clostridium perfringens demonstrate dynamic conformational change.
Authors: Tamai, E. / Katayama, S. / Sekiya, H. / Nariya, H. / Kamitori, S.
History
DepositionMar 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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: Probable surface protein


Theoretical massNumber of molelcules
Total (without water)36,4641
Polymers36,4641
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.400, 141.330, 61.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Probable surface protein / pili protein


Mass: 36464.484 Da / Num. of mol.: 1 / Fragment: UNP residues 30-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens str. 13 (bacteria)
Strain: 13 / Gene: CPE0156 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XP10
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.06M Magnesium chloride hexahydrate, 0.06M Calcium chloride dihydrate, 0.1M Tris (base), 0.1M BICINE, 20% v/v PEG 500* MME, 10 % w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.14→18.76 Å / Num. obs: 22094 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 22.86
Reflection shellResolution: 2.14→2.2 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.01 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→18.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.681 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25123 1129 5.1 %RANDOM
Rwork0.21123 ---
obs0.21325 20965 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.056 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.14→18.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 0 150 2525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022414
X-RAY DIFFRACTIONr_bond_other_d00.022196
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.9553268
X-RAY DIFFRACTIONr_angle_other_deg0.59635153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2695301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.67526.916107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99715440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.216151
X-RAY DIFFRACTIONr_chiral_restr0.0630.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022658
X-RAY DIFFRACTIONr_gen_planes_other00.02427
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3964.6451210
X-RAY DIFFRACTIONr_mcbond_other2.3954.6431209
X-RAY DIFFRACTIONr_mcangle_it3.7256.9491509
X-RAY DIFFRACTIONr_mcangle_other3.7246.9511510
X-RAY DIFFRACTIONr_scbond_it2.6234.9191203
X-RAY DIFFRACTIONr_scbond_other2.6234.9191203
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1567.2411758
X-RAY DIFFRACTIONr_long_range_B_refined6.41354.7162700
X-RAY DIFFRACTIONr_long_range_B_other6.3754.5592675
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 88 -
Rwork0.308 1495 -
obs--99.81 %

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