[English] 日本語
Yorodumi
- PDB-8auc: Structure of peptidoglycan hydrolase Cg1735 from Corynebacterium ... -

+
Open data


ID or keywords:

Loading...

-
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 / homologyNlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Papain-like cysteine peptidase superfamily / hydrolase activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 50 through 238 or resid 243 through 410 or resid 460 through 600 or resid 701))A50 - 238
121(chain A and (resid 50 through 238 or resid 243 through 410 or resid 460 through 600 or resid 701))A243 - 410
131(chain A and (resid 50 through 238 or resid 243 through 410 or resid 460 through 600 or resid 701))A460 - 600
141(chain A and (resid 50 through 238 or resid 243 through 410 or resid 460 through 600 or resid 701))A701
211(chain B and (resid 50 through 125 or resid 146 through 600 or resid 701))B50 - 125
221(chain B and (resid 50 through 125 or resid 146 through 600 or resid 701))B146 - 600
231(chain B and (resid 50 through 125 or resid 146 through 600 or resid 701))B701

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

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

-
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

-
Phasing

PhasingMethod: SAD

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more