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- PDB-8au6: Structure of Corynebacterium glutamicum Cg1604, a cell division r... -

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Basic information

Entry
Database: PDB / ID: 8au6
TitleStructure of Corynebacterium glutamicum Cg1604, a cell division regulator
ComponentsRegulatory protein Cg1604
KeywordsCELL CYCLE / bacterial cell division / peptidoglycan hydrolysis / regulatory protein
Function / homologyCopper transporter MctB / Copper transport outer membrane protein, MctB / copper ion homeostasis / metal ion binding / membrane / Copper transporter
Function and homology information
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein Cg1604
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8432
Polymers32,8021
Non-polymers401
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-10 kcal/mol
Surface area11980 Å2
Unit cell
Length a, b, c (Å)66.780, 105.500, 70.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-532-

HOH

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Components

#1: Protein Regulatory protein Cg1604


Mass: 32802.434 Da / Num. of mol.: 1
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: Cgl1416 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NQL8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 35.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 30 % (w/v) PEG 4K, 0.2 M MgCl2, 0.1 M TRIS pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979261 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979261 Å / Relative weight: 1
ReflectionResolution: 2→44.1 Å / Num. obs: 17209 / % possible obs: 99.7 % / Redundancy: 14.6 % / CC1/2: 0.999 / Rpim(I) all: 0.035 / Net I/σ(I): 16.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 11.5 % / Num. unique obs: 1207 / CC1/2: 0.551 / Rpim(I) all: 0.642 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→44.04 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1625 5 %
Rwork0.194 30848 -
obs0.1957 17164 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.52 Å2 / Biso mean: 48.0537 Å2 / Biso min: 29.37 Å2
Refinement stepCycle: final / Resolution: 2→44.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 1 109 1912
Biso mean--64.04 47.62 -
Num. residues----248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.060.46861270.39822470259796
2.06-2.120.38791360.3325862722100
2.12-2.20.34321350.273625682703100
2.2-2.290.29181370.249125842721100
2.29-2.390.2441380.235525922730100
2.39-2.520.27031340.198525852719100
2.52-2.680.2751400.209925492689100
2.68-2.880.21111380.202825792717100
2.88-3.170.26041380.205725892727100
3.17-3.630.22011350.181725842719100
3.63-4.570.16181380.157625642702100
4.57-44.040.18571290.152125982727100
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)
19.5767-3.9238-2.42763.90171.191.72640.20090.37320.4418-0.3162-0.13180.4026-0.3605-0.2579-0.07690.94610.031-0.07060.30910.01730.4966-7.637463.624315.5141
21.5978-1.2481-0.33764.02430.33471.92770.0071-0.0158-0.0248-0.15360.0726-0.06120.25010.0934-0.0690.5048-0.0197-0.02940.2414-0.01250.250217.045938.70721.9825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 76 )A46 - 76
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 293 )A77 - 293

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