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- PDB-8aud: Structure of peptidoglycan hydrolase Cg1735 from Corynebacterium ... -

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Basic information

Entry
Database: PDB / ID: 8aud
TitleStructure of peptidoglycan hydrolase Cg1735 from Corynebacterium glutamicum, orthorhombic crystal form
ComponentsCell wall-associated hydrolases (Invasion-associated proteins)
KeywordsCELL CYCLE / bacterial cell division / peptidoglycan hydrolysis / regulatory protein
Function / homology: / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / cysteine-type peptidase activity / Papain-like cysteine peptidase superfamily / proteolysis / Cell wall-associated hydrolases (Invasion-associated proteins)
Function and homology information
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsGaday, Q. / Wehenkel, A.M. / Alzari, P.M.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-13-JSV8-0003, ANR-18-CE92-0003 France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: FtsEX-independent control of RipA-mediated cell separation in Corynebacteriales.
Authors: Gaday, Q. / Megrian, D. / Carloni, G. / Martinez, M. / Sokolova, B. / Ben Assaya, M. / Legrand, P. / Brule, S. / Haouz, A. / Wehenkel, A.M. / Alzari, P.M.
History
DepositionAug 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Cell wall-associated hydrolases (Invasion-associated proteins)
B: Cell wall-associated hydrolases (Invasion-associated proteins)


Theoretical massNumber of molelcules
Total (without water)123,7182
Polymers123,7182
Non-polymers00
Water00
1
A: Cell wall-associated hydrolases (Invasion-associated proteins)


Theoretical massNumber of molelcules
Total (without water)61,8591
Polymers61,8591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell wall-associated hydrolases (Invasion-associated proteins)


Theoretical massNumber of molelcules
Total (without water)61,8591
Polymers61,8591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.572, 123.083, 209.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell wall-associated hydrolases (Invasion-associated proteins)


Mass: 61858.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The register is unknown for helix 344-362 in chain A and helix 350-365 in chain B. These residues were modeled as poly-alanine (UNK).,The register is unknown for helix 344-362 in chain A and ...Details: The register is unknown for helix 344-362 in chain A and helix 350-365 in chain B. These residues were modeled as poly-alanine (UNK).,The register is unknown for helix 344-362 in chain A and helix 350-365 in chain B. These residues were modeled as poly-alanine (UNK).,The register is unknown for helix 344-362 in chain A and helix 350-365 in chain B. These residues were modeled as poly-alanine (UNK).
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: Cgl1538 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NQA0

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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: 4.97 Å3/Da / Density % sol: 75.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 2.4 M (NH4)2SO4, 0.1 M Na3 citrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98112 Å / Relative weight: 1
ReflectionResolution: 4.5→61.54 Å / Num. obs: 15441 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.992 / Rpim(I) all: 0.117 / Net I/σ(I): 5.5
Reflection shellResolution: 4.5→5.03 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4293 / CC1/2: 0.931 / Rpim(I) all: 0.342 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AUC

8auc


Resolution: 4.5→61.54 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3071 585 5.08 %
Rwork0.2782 --
obs0.2797 11523 74.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.5→61.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5142 0 0 0 5142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055190
X-RAY DIFFRACTIONf_angle_d1.0697031
X-RAY DIFFRACTIONf_dihedral_angle_d17.6241879
X-RAY DIFFRACTIONf_chiral_restr0.054817
X-RAY DIFFRACTIONf_plane_restr0.008950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5-4.950.2846890.21131627X-RAY DIFFRACTION46
4.95-5.670.32831360.26012317X-RAY DIFFRACTION65
5.67-7.140.34091660.30623208X-RAY DIFFRACTION88
7.14-61.540.29151940.28993786X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82980.0737-0.7131.75781.3871.67970.00960.343-0.0487-0.06550.0839-0.1118-0.0998-0.06290.65591.1141-0.0017-0.03380.0045-0.04290.568765.7059-38.8115-34.8818
23.7706-0.1249-0.9811.4527-0.71573.11120.0019-0.1591-0.3477-0.32540.12210.28950.60130.1494-0.06690.29420.0314-0.0620.1739-0.00850.282663.2246-44.58-13.3094
31.2528-1.24451.38274.696-5.59385.97720.2271-0.31930.1738-0.55720.34220.53340.5158-0.06070.27230.8681-0.063-0.03980.51560.02720.590125.3743-24.0024-37.8644
40.89760.1802-0.37220.83420.78360.97710.22020.01230.0216-0.41070.19450.193-0.62120.07160.07220.69970.00230.03110.28410.21540.393528.6923-18.4004-16.2152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 238)
2X-RAY DIFFRACTION2chain 'A' and (resid 344 through 600 )
3X-RAY DIFFRACTION3chain 'B' and (resid 46 through 238 )
4X-RAY DIFFRACTION4chain 'B' and (resid 350 through 600)

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