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- PDB-7d6t: X-ray structure of Clostridium perfringens sortase C with the C-t... -

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Basic information

Entry
Database: PDB / ID: 7d6t
TitleX-ray structure of Clostridium perfringens sortase C with the C-terminal cell wall sorting motif.
ComponentsSortase family protein
KeywordsTRANSFERASE / cysteine transpeptidase
Function / homologySortase C / Sortase family / Sortase domain superfamily / Sortase domain / hydrolase activity / membrane / Sortase family protein
Function and homology information
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsKamitori, S. / Tamai, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06087 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: X-ray structures of Clostridium perfringens sortase C with C-terminal cell wall sorting motif of LPST demonstrate role of subsite for substrate-binding and structural variations of catalytic site.
Authors: Tamai, E. / Sekiya, H. / Nariya, H. / Katayama, S. / Kamitori, S.
History
DepositionOct 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Sortase family protein
B: Sortase family protein


Theoretical massNumber of molelcules
Total (without water)49,6622
Polymers49,6622
Non-polymers00
Water3,495194
1
A: Sortase family protein


Theoretical massNumber of molelcules
Total (without water)24,8311
Polymers24,8311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sortase family protein


Theoretical massNumber of molelcules
Total (without water)24,8311
Polymers24,8311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.230, 62.690, 77.690
Angle α, β, γ (deg.)90.00, 102.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sortase family protein / sortase C


Mass: 24830.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain SM101 / Type A) (bacteria)
Gene: CPR_0146 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0SWL7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 1.99 Å3/Da / Density % sol: 38.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) PEG 4000, 200mM LiSO4, 100mM Tris-HCl, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.68→19.02 Å / Num. obs: 43526 / % possible obs: 97.6 % / Redundancy: 2.4 % / CC1/2: 0.998 / Net I/σ(I): 12.56
Reflection shellResolution: 1.68→1.72 Å / Num. unique obs: 3217 / CC1/2: 0.839

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IXZ

6ixz


Resolution: 1.68→19.02 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.697 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22033 2197 5 %RANDOM
Rwork0.1554 ---
obs0.15873 41328 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.313 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.02 Å2
2---0.17 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.68→19.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2966 0 0 194 3160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133017
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172822
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.6394096
X-RAY DIFFRACTIONr_angle_other_deg1.3131.5866585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3785371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91225.608148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66115544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.395156
X-RAY DIFFRACTIONr_chiral_restr0.0740.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023326
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02540
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_it3.9442.6591490
X-RAY DIFFRACTIONr_mcbond_other3.8531489
X-RAY DIFFRACTIONr_mcangle_it4.59841859
X-RAY DIFFRACTIONr_mcangle_other4.5976.91860
X-RAY DIFFRACTIONr_scbond_it5.3163.2521527
X-RAY DIFFRACTIONr_scbond_other5.3141528
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.074.6622238
X-RAY DIFFRACTIONr_long_range_B_refined5.8723839
X-RAY DIFFRACTIONr_long_range_B_other5.8523771
X-RAY DIFFRACTIONr_rigid_bond_restr5.57233017
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 159 -
Rwork0.268 3030 -
obs--98.46 %

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