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- PDB-5b23: X-ray Structure of Clostridium Perfringens Sortase B -

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Basic information

Entry
Database: PDB / ID: 5b23
TitleX-ray Structure of Clostridium Perfringens Sortase B
ComponentsUncharacterized protein Sortase B
KeywordsHYDROLASE / transpeptidase / sortase / Clostridium Perfringens
Function / homology
Function and homology information


Sortase B, Firmicutes / Sortase B family / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKamitori, S. / Yoshida, H. / Tamai, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K06973 Japan
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: X-ray structure of Clostridium perfringens sortase B cysteine transpeptidase
Authors: Tamai, E. / Sekiya, H. / Maki, J. / Nariya, H. / Yoshida, H. / Kamitori, S.
History
DepositionDec 28, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Sortase B
B: Uncharacterized protein Sortase B


Theoretical massNumber of molelcules
Total (without water)55,5822
Polymers55,5822
Non-polymers00
Water1,928107
1
A: Uncharacterized protein Sortase B


Theoretical massNumber of molelcules
Total (without water)27,7911
Polymers27,7911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein Sortase B


Theoretical massNumber of molelcules
Total (without water)27,7911
Polymers27,7911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.200, 96.400, 58.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Uncharacterized protein Sortase B


Mass: 27790.756 Da / Num. of mol.: 2 / Fragment: UNP residues 24-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain 13 / Type A) (bacteria)
Strain: 13 / Type A / Gene: CPE0513 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XN25
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.3 Å3/Da / Density % sol: 41.86 % / Description: prismatic shape
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.2 M Sodium nitrate, 205 w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.2 Å / Num. obs: 24626 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.29
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 4.66 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UX7

4ux7


Resolution: 2.2→48.2 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.717 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27495 1250 5.1 %RANDOM
Rwork0.22393 ---
obs0.22656 23338 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.541 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 0 107 3155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193110
X-RAY DIFFRACTIONr_bond_other_d00.022880
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.9284180
X-RAY DIFFRACTIONr_angle_other_deg0.58536632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.15364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39925.495182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.15915574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4441512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023586
X-RAY DIFFRACTIONr_gen_planes_other00.02778
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 84 -
Rwork0.282 1729 -
obs--99.83 %

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