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- PDB-6ixy: X-ray structure of major pilin from C. perfringens SM101 -

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Basic information

Entry
Database: PDB / ID: 6ixy
TitleX-ray structure of major pilin from C. perfringens SM101
Componentspilin
KeywordsSTRUCTURAL PROTEIN / major pilin / fiber protein
Function / homology
Function and homology information


Gram-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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative surface protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsKamitori, S. / Tamai, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science18K06087 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
DepositionDec 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Oct 16, 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: pilin
B: pilin
C: pilin
D: pilin


Theoretical massNumber of molelcules
Total (without water)209,2884
Polymers209,2884
Non-polymers00
Water1,78399
1
A: pilin


Theoretical massNumber of molelcules
Total (without water)52,3221
Polymers52,3221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: pilin


Theoretical massNumber of molelcules
Total (without water)52,3221
Polymers52,3221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: pilin


Theoretical massNumber of molelcules
Total (without water)52,3221
Polymers52,3221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: pilin


Theoretical massNumber of molelcules
Total (without water)52,3221
Polymers52,3221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.140, 111.830, 118.590
Angle α, β, γ (deg.)90.00, 107.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
pilin / Putative surface protein


Mass: 52321.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain SM101 / Type A) (bacteria)
Gene: CPR_0145 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0SWL8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 4% v/v Tacsimate buffer pH 4.0 (73mM malonic acid, 10mM ammonium citrate tribasic, 5mM succinic acid, 12mM D,L-malic acid, 16mM sodium acetate trihydrate, 20mM sodium formate, 6.4mM ammonium ...Details: 4% v/v Tacsimate buffer pH 4.0 (73mM malonic acid, 10mM ammonium citrate tribasic, 5mM succinic acid, 12mM D,L-malic acid, 16mM sodium acetate trihydrate, 20mM sodium formate, 6.4mM ammonium tartrate dibasic), 12% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→48.71 Å / Num. obs: 69104 / % possible obs: 99.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.8
Reflection shellResolution: 2.72→2.79 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5092

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XCC

5xcc


Resolution: 2.72→48.71 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.855 / SU B: 13.343 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R: 0.766 / ESU R Free: 0.354 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27554 3502 5.1 %RANDOM
Rwork0.22728 ---
obs0.22977 65602 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.106 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0.18 Å2
2--0.21 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.72→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13922 0 0 99 14021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0214142
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213350
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.96419158
X-RAY DIFFRACTIONr_angle_other_deg0.776331002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.51751800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.37227.082610
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.217152576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.604154
X-RAY DIFFRACTIONr_chiral_restr0.070.22204
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216192
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022932
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.72→2.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 230 -
Rwork0.308 4862 -
obs--99.59 %

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