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- PDB-6ixz: X-ray structure of sortase C from Clostridium perfringens SM101 -

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Basic information

Entry
Database: PDB / ID: 6ixz
TitleX-ray structure of sortase C from Clostridium perfringens SM101
ComponentsSortase family protein
KeywordsTRANSFERASE / sortase / cysteine transpeptidase
Function / homology
Function and homology information


hydrolase activity / membrane
Similarity search - Function
Sortase C / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Sortase family protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsKamitori, S. / Tamai, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
18K06087 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortase family protein
B: Sortase family protein


Theoretical massNumber of molelcules
Total (without water)50,0722
Polymers50,0722
Non-polymers00
Water1,51384
1
A: Sortase family protein


Theoretical massNumber of molelcules
Total (without water)25,0361
Polymers25,0361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sortase family protein


Theoretical massNumber of molelcules
Total (without water)25,0361
Polymers25,0361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.450, 63.410, 76.530
Angle α, β, γ (deg.)90.00, 101.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sortase family protein


Mass: 25036.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain SM101 / Type A) (bacteria)
Strain: SM101 / Type A / Gene: CPR_0146 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0SWL7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.98 Å3/Da / Density % sol: 37.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM MMT buffer pH 6.5 (20mM L-malic acid, 40mM MES, 40mM Tris), 25% w/v PEG 1500

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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 / Detector: IMAGE PLATE / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→19.63 Å / Num. obs: 27084 / % possible obs: 98.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.8
Reflection shellResolution: 1.98→2.03 Å / Rmerge(I) obs: 0.336 / Num. unique obs: 1996

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D7W

4d7w


Resolution: 1.98→19.63 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.892 / SU B: 5.455 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28344 1357 5 %RANDOM
Rwork0.23124 ---
obs0.23395 25726 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.154 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20.08 Å2
2---0.14 Å20 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.98→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 0 84 3008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192974
X-RAY DIFFRACTIONr_bond_other_d00.022856
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.9814037
X-RAY DIFFRACTIONr_angle_other_deg0.66636605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.345364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56726.241141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.62115535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.703156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023331
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02611
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: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 96 -
Rwork0.266 1875 -
obs--97.43 %

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