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- PDB-8gsx: X-ray structure of Clostridium perfringens pili protein B collage... -

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Basic information

Entry
Database: PDB / ID: 8gsx
TitleX-ray structure of Clostridium perfringens pili protein B collagen-binding domains
Componentspili protein
KeywordsPROTEIN FIBRIL / pili
Function / homology
Function and homology information


cell adhesion / extracellular region / membrane
Similarity search - Function
Immunoglobulin-like - #740 / Fibrogen-binding domain 1 / Prealbumin-like fold domain / Prealbumin-like fold domain / Adhesion domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Prealbumin-like fold domain-containing protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.86 Å
AuthorsKamitori, S. / Yamada, M. / Tamai, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K0687 Japan
CitationJournal: Febs Lett. / Year: 2023
Title: Structural and biochemical characterization of Clostridium perfringens pili protein B collagen-binding domains.
Authors: Tamai, E. / Yamada, M. / Ishida, T. / Arimura, N. / Matsunami, R. / Sekiya, H. / Kamitori, S.
History
DepositionSep 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pili protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7046
Polymers38,4091
Non-polymers2955
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.390, 127.390, 163.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein pili protein


Mass: 38408.871 Da / Num. of mol.: 1 / Fragment: collagen-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: 13 / Type A / Gene: CPE0155 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XP11
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.98 Å3/Da / Density % sol: 81.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 100 mM sodium acetate pH4.8, 400 mM ammonium sulfate, 16-19% w/v PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.86→48.83 Å / Num. obs: 18588 / % possible obs: 99.5 % / Redundancy: 6.2 % / CC1/2: 0.994 / Net I/σ(I): 10.13
Reflection shellResolution: 2.86→2.93 Å / Num. unique obs: 1330 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.86→48.83 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.865 / SU B: 12.655 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.349 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2859 913 4.9 %RANDOM
Rwork0.2524 ---
obs0.25402 17675 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.729 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å20 Å2
2--0.45 Å2-0 Å2
3----1.45 Å2
Refinement stepCycle: 1 / Resolution: 2.86→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 20 5 2097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132127
X-RAY DIFFRACTIONr_bond_other_d0.0040.0151959
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.6552871
X-RAY DIFFRACTIONr_angle_other_deg1.0491.5894525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8955255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58423.103116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.5515366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7951512
X-RAY DIFFRACTIONr_chiral_restr0.0580.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022411
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02480
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_it4.069.7721037
X-RAY DIFFRACTIONr_mcbond_other4.0369.761031
X-RAY DIFFRACTIONr_mcangle_it6.43814.6271283
X-RAY DIFFRACTIONr_mcangle_other6.43614.6331284
X-RAY DIFFRACTIONr_scbond_it4.30910.0271090
X-RAY DIFFRACTIONr_scbond_other4.30710.0281091
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.88114.8881589
X-RAY DIFFRACTIONr_long_range_B_refined10.00183.9981522
X-RAY DIFFRACTIONr_long_range_B_other9.99884.11523
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.86→2.935 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 75 -
Rwork0.385 1255 -
obs--99.92 %

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