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

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Basic information

Entry
Database: PDB / ID: 8auc
TitleStructure of peptidoglycan hydrolase Cg1735 from Corynebacterium glutamicum, trigonal 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 / TETRACHLOROPLATINATE(II) / Cell wall-associated hydrolases (Invasion-associated proteins)
Function and homology information
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsGaday, Q. / Wehenkel, A.M. / Alzari, P.M. / Legrand, P.
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 1.1Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell wall-associated hydrolases (Invasion-associated proteins)
B: Cell wall-associated hydrolases (Invasion-associated proteins)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,0404
Polymers125,3662
Non-polymers6742
Water00
1
A: Cell wall-associated hydrolases (Invasion-associated proteins)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0202
Polymers62,6831
Non-polymers3371
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell wall-associated hydrolases (Invasion-associated proteins)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0202
Polymers62,6831
Non-polymers3371
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-72 kcal/mol
Surface area53540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.580, 230.580, 416.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 50 through 238 or resid 243 through 410 or resid 460 through 600 or resid 701))
21(chain B and (resid 50 through 125 or resid 146 through 600 or resid 701))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUASPASP(chain A and (resid 50 through 238 or resid 243 through 410 or resid 460 through 600 or resid 701))AA50 - 23850 - 238
12GLNGLNILEILE(chain A and (resid 50 through 238 or resid 243 through 410 or resid 460 through 600 or resid 701))AA243 - 410243 - 410
13ASPASPILEILE(chain A and (resid 50 through 238 or resid 243 through 410 or resid 460 through 600 or resid 701))AA460 - 600460 - 600
14PC4PC4PC4PC4(chain A and (resid 50 through 238 or resid 243 through 410 or resid 460 through 600 or resid 701))AC701
21LEULEUGLYGLY(chain B and (resid 50 through 125 or resid 146 through 600 or resid 701))BB50 - 12550 - 125
22GLNGLNILEILE(chain B and (resid 50 through 125 or resid 146 through 600 or resid 701))BB146 - 600146 - 600
23PC4PC4PC4PC4(chain B and (resid 50 through 125 or resid 146 through 600 or resid 701))BD701

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Components

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


Mass: 62683.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: Cgl1538 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NQA0
#2: Chemical ChemComp-PC4 / TETRACHLOROPLATINATE(II)


Mass: 336.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl4Pt
Has ligand of interestN

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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

Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 1 M (NH4)2H Citrate, 0.1 M Na Acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07188 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07188 Å / Relative weight: 1
ReflectionResolution: 3.5→49.6 Å / Num. obs: 54157 / % possible obs: 99.6 % / Redundancy: 115.6 % / Biso Wilson estimate: 78.68 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.049 / Net I/σ(I): 13.4
Reflection shellResolution: 3.5→3.58 Å / Redundancy: 101.4 % / Num. unique obs: 3903 / CC1/2: 0.52 / Rpim(I) all: 7.886 / % possible all: 98.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
SHELXphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.5→49.57 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2602 2891 4.92 %
Rwork0.2261 55839 -
obs0.2278 30724 56.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 220.32 Å2 / Biso mean: 89.6708 Å2 / Biso min: 27.77 Å2
Refinement stepCycle: final / Resolution: 3.5→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7197 0 2 0 7199
Biso mean--97.91 --
Num. residues----967
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2772X-RAY DIFFRACTION1.659TORSIONAL
12B2772X-RAY DIFFRACTION1.659TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.550.3024730.3127984105721
3.55-3.610.2815670.29121088115523
3.61-3.680.3194640.26341168123225
3.68-3.750.2591620.22031278134027
3.75-3.830.2514640.21411311137528
3.83-3.910.2523800.25931467154731
3.91-40.2523870.23511517160432
4-4.10.2319760.21811619169534
4.1-4.210.23061200.22471656177636
4.21-4.340.2355920.19141921201340
4.34-4.480.20671140.19292168228246
4.48-4.640.2541430.19712344248750
4.64-4.820.25281130.20782741285457
4.82-5.040.27241410.21072926306761
5.04-5.310.2721830.23373483366674
5.31-5.640.31092170.28054541475896
5.64-6.070.31882620.279147184980100
6.07-6.680.34012470.244347474994100
6.68-7.650.26792390.222447194958100
7.65-9.620.18812300.186247735003100
9.62-49.570.24812170.22874670488798
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)
10.50930.0864-0.06150.028-0.15732.1640.0283-0.2585-0.094-0.3249-0.0139-0.1480.4470.1713-0.27110.97040.0991-0.04410.6032-0.12680.7383-69.8438-16.60062.8862
20.0906-0.26960.11720.9623-0.43290.2491-0.2126-0.0368-0.0505-0.28070.1424-0.1576-0.00250.16230.10981.8001-0.0506-0.0430.38540.0240.64-78.1197-58.4125-44.4286
30.1664-0.05440.110.0285-0.02480.09220.352-0.3396-0.0215-0.232-0.07810.22540.5288-0.6243-0.07921.1681-0.5651-0.1090.51060.26650.5129-92.7847-12.2012-47.9577
40.1814-0.48290.11280.0452-0.0630.03030.05740.169-0.0535-0.20230.0795-0.0612-0.2771-0.2519-0.1410.9013-0.4098-0.00690.43120.05550.4659-94.241-1.8603-64.6759
50.54170.55410.36980.35130.39130.17190.2424-0.474-0.09160.5461-0.22390.20580.3795-0.5597-0.18060.8772-0.7424-0.00831.50130.08810.8434-126.4716-29.0338-18.8022
60.14590.1260.13920.14590.08350.25290.1954-0.1186-0.2707-0.44390.154-0.28520.91730.01810.2091.6703-0.2372-0.1841-0.0854-0.380.3406-79.572-19.8157-15.7789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 240 )A41 - 240
2X-RAY DIFFRACTION2chain 'A' and (resid 241 through 385 )A241 - 385
3X-RAY DIFFRACTION3chain 'A' and (resid 386 through 600 )A386 - 600
4X-RAY DIFFRACTION4chain 'B' and (resid 24 through 238 )B24 - 238
5X-RAY DIFFRACTION5chain 'B' and (resid 243 through 385 )B243 - 385
6X-RAY DIFFRACTION6chain 'B' and (resid 386 through 600 )B386 - 600

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