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- PDB-7cfl: X-ray structure of autolysin Acd24020 catalytic domain from Clost... -

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Basic information

Entry
Database: PDB / ID: 7cfl
TitleX-ray structure of autolysin Acd24020 catalytic domain from Clostridium difficile
ComponentsPutative cell wall hydrolase phosphatase-associated protein
KeywordsHYDROLASE / endopeptidase / autolysin
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / hydrolase activity
Similarity search - Function
Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / NlpC/P60 domain profile. / SH3-like domain, bacterial-type / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Papain-like cysteine peptidase superfamily / SH3-like domain superfamily
Similarity search - Domain/homology
CITRATE ANION / Putative cell wall hydrolase phosphatase-associated protein
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsKamitori, S. / Tamai, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06087 Japan
CitationJournal: Mol.Microbiol. / Year: 2021
Title: Structural and biochemical characterizations of the novel autolysin Acd24020 from Clostridioides difficile and its full-function catalytic domain as a lytic enzyme.
Authors: Sekiya, H. / Tamai, E. / Kawasaki, J. / Murakami, K. / Kamitori, S.
History
DepositionJun 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: Putative cell wall hydrolase phosphatase-associated protein
B: Putative cell wall hydrolase phosphatase-associated protein
C: Putative cell wall hydrolase phosphatase-associated protein
D: Putative cell wall hydrolase phosphatase-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4728
Polymers60,7164
Non-polymers7564
Water4,432246
1
A: Putative cell wall hydrolase phosphatase-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3682
Polymers15,1791
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint0 kcal/mol
Surface area6100 Å2
MethodPISA
2
B: Putative cell wall hydrolase phosphatase-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3682
Polymers15,1791
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-1 kcal/mol
Surface area5900 Å2
MethodPISA
3
C: Putative cell wall hydrolase phosphatase-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3682
Polymers15,1791
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint0 kcal/mol
Surface area5920 Å2
MethodPISA
4
D: Putative cell wall hydrolase phosphatase-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3682
Polymers15,1791
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-1 kcal/mol
Surface area5870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.440, 55.210, 57.110
Angle α, β, γ (deg.)104.86, 112.64, 90.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative cell wall hydrolase phosphatase-associated protein / autolysin


Mass: 15178.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: CD630_24020 / Production host: Escherichia coli (E. coli)
References: UniProt: Q181Y8, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 200 mM ammonium citrate dibasic, 20% (w/v) polyethylene glycol 3,350

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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 2M / Detector: PIXEL / Date: Jun 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→36.97 Å / Num. obs: 73725 / % possible obs: 99.2 % / Redundancy: 1.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.044 / Net I/σ(I): 9.4
Reflection shellResolution: 1.56→1.6 Å / Rmerge(I) obs: 0.05 / Num. unique obs: 5198 / CC1/2: 0.961

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H41

3h41


Resolution: 1.56→36.97 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.985 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25844 3667 5 %RANDOM
Rwork0.198 ---
obs0.20108 69608 94.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.501 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0.17 Å20.3 Å2
2---0.45 Å2-0.22 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.56→36.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3759 0 52 246 4057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133948
X-RAY DIFFRACTIONr_bond_other_d0.0020.0183539
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.6345342
X-RAY DIFFRACTIONr_angle_other_deg1.451.5838212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1525510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.29220.576191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14715641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3161528
X-RAY DIFFRACTIONr_chiral_restr0.0870.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024522
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02902
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_it3.6842.6491989
X-RAY DIFFRACTIONr_mcbond_other3.6814.4611988
X-RAY DIFFRACTIONr_mcangle_it4.2273.9762480
X-RAY DIFFRACTIONr_mcangle_other4.2265.2932481
X-RAY DIFFRACTIONr_scbond_it4.7662.9741959
X-RAY DIFFRACTIONr_scbond_other4.76518.4021958
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4634.322851
X-RAY DIFFRACTIONr_long_range_B_refined5.3484417
X-RAY DIFFRACTIONr_long_range_B_other5.3454392
X-RAY DIFFRACTIONr_rigid_bond_restr6.45133948
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 271 -
Rwork0.263 4927 -
obs--90.86 %

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