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- PDB-5xcc: X-ray structure of Clostridium perfringens pili protein CppA -

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Basic information

Entry
Database: PDB / ID: 5xcc
TitleX-ray structure 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable surface protein
B: Probable surface protein


Theoretical massNumber of molelcules
Total (without water)104,7582
Polymers104,7582
Non-polymers00
Water4,594255
1
A: Probable surface protein


Theoretical massNumber of molelcules
Total (without water)52,3791
Polymers52,3791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable surface protein


Theoretical massNumber of molelcules
Total (without water)52,3791
Polymers52,3791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.340, 71.330, 228.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable surface protein / pili protein


Mass: 52379.012 Da / Num. of mol.: 2 / Fragment: UNP residues 30-488
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.: 255 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Sodium formate, 0.1M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Sodium potassium tartrate tetrahydrate, 0.1M Sodium oxamate, 0.1M Imidazole, o.1M MES monohydrate ...Details: 0.1M Sodium formate, 0.1M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Sodium potassium tartrate tetrahydrate, 0.1M Sodium oxamate, 0.1M Imidazole, o.1M MES monohydrate (acid), 20% v/v Ethylene glycol, 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→114.38 Å / Num. obs: 37465 / % possible obs: 99.4 % / Redundancy: 5.28 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.08
Reflection shellResolution: 2.48→2.54 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.71 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XCB

5xcb


Resolution: 2.48→114.38 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.909 / SU B: 13.506 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R: 0.608 / ESU R Free: 0.311 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27182 1867 5 %RANDOM
Rwork0.2275 ---
obs0.22974 35598 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.48→114.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7018 0 0 255 7273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.027134
X-RAY DIFFRACTIONr_bond_other_d00.026498
X-RAY DIFFRACTIONr_angle_refined_deg0.7571.9559654
X-RAY DIFFRACTIONr_angle_other_deg0.544315244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3235906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31226.987312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.665151284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.65152
X-RAY DIFFRACTIONr_chiral_restr0.0470.21106
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027928
X-RAY DIFFRACTIONr_gen_planes_other00.021274
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_it1.1114.7363630
X-RAY DIFFRACTIONr_mcbond_other1.1114.7353629
X-RAY DIFFRACTIONr_mcangle_it1.9077.14534
X-RAY DIFFRACTIONr_mcangle_other1.9077.1014535
X-RAY DIFFRACTIONr_scbond_it1.0464.8513504
X-RAY DIFFRACTIONr_scbond_other1.0464.8513505
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7867.2085121
X-RAY DIFFRACTIONr_long_range_B_refined3.35954.97722
X-RAY DIFFRACTIONr_long_range_B_other3.34154.8757696
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.48→2.544 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 134 -
Rwork0.343 2572 -
obs--98.47 %

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