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- PDB-8gsy: X-ray structure of Clostridium perfringens pili protein B N-termi... -

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Basic information

Entry
Database: PDB / ID: 8gsy
TitleX-ray structure of Clostridium perfringens pili protein B N-terminal domain
ComponentsPeptidoglycan bound protein
KeywordsPROTEIN FIBRIL / Pili protein
Function / homologyCollagen binding domain / Collagen binding domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / collagen binding / cell adhesion / extracellular region / membrane / Peptidoglycan bound protein
Function and homology information
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKamitori, S. / Yamada, M. / Tamai, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06087 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 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan bound protein
B: Peptidoglycan bound protein


Theoretical massNumber of molelcules
Total (without water)32,7372
Polymers32,7372
Non-polymers00
Water1,874104
1
A: Peptidoglycan bound protein


Theoretical massNumber of molelcules
Total (without water)16,3681
Polymers16,3681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidoglycan bound protein


Theoretical massNumber of molelcules
Total (without water)16,3681
Polymers16,3681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.080, 39.080, 290.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Peptidoglycan bound protein


Mass: 16368.459 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: NCTC8081_03081 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2X3IRB0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.96 Å3/Da / Density % sol: 37.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 50 mM bis-tris pH 6.5, 50 mM ammonium sulfate, 30% v/v pentaerythritol ethoxylate (15/4 EO/OH)

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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 6M / Detector: PIXEL / Date: Mar 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→48.48 Å / Num. obs: 39168 / % possible obs: 99.98 % / Redundancy: 9.4 % / CC1/2: 0.999 / Net I/σ(I): 23.23
Reflection shellResolution: 1.55→1.59 Å / Num. unique obs: 2809 / CC1/2: 0.789

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GSX

8gsx


Resolution: 1.55→48.48 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.51 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23963 1935 4.9 %RANDOM
Rwork0.18393 ---
obs0.1868 37233 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.172 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å20 Å2
2--0.13 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 1.55→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 0 104 2092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132020
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161936
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.6462730
X-RAY DIFFRACTIONr_angle_other_deg1.3441.5964480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8745250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92225100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5815370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.025156
X-RAY DIFFRACTIONr_chiral_restr0.0630.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022288
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02428
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_it3.5432.8371006
X-RAY DIFFRACTIONr_mcbond_other3.5416.3081005
X-RAY DIFFRACTIONr_mcangle_it4.2744.281254
X-RAY DIFFRACTIONr_mcangle_other4.27333.851255
X-RAY DIFFRACTIONr_scbond_it4.8773.3941014
X-RAY DIFFRACTIONr_scbond_other4.8775.3691014
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.59421.5721476
X-RAY DIFFRACTIONr_long_range_B_refined5.8061392
X-RAY DIFFRACTIONr_long_range_B_other5.8041393
X-RAY DIFFRACTIONr_rigid_bond_restr6.25832020
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 133 -
Rwork0.245 2676 -
obs--99.86 %

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