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- PDB-8bve: MoeA2 from Corynebacterium glutamicum -

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Basic information

Entry
Database: PDB / ID: 8bve
TitleMoeA2 from Corynebacterium glutamicum
ComponentsMolybdopterin molybdenumtransferase
KeywordsCELL CYCLE / Molybdopterin molybdotransferase / cell division / gephyrin-like protein / Corynebacteriales
Function / homology
Function and homology information


molybdopterin cofactor biosynthetic process / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / Mo-molybdopterin cofactor biosynthetic process / metal ion binding
Similarity search - Function
MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain
Similarity search - Domain/homology
CITRIC ACID / Molybdopterin molybdenumtransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsMartinez, M. / Haouz, A. / Wehenkel, A.M. / Alzari, P.M.
Funding support France, Uruguay, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0017 France
Agence Nationale de la Recherche (ANR)ANR-21-CE11-0003 France
Agencia Nacional de Investigacion e Innovacion (ANII)FCE_1_2019_1_155569Uruguay
CitationJournal: Biorxiv / Year: 2023
Title: Eukaryotic-like gephyrin and cognate membrane receptor coordinate corynebacterial cell division and polar elongation.
Authors: Martinez, M. / Petit, J. / Leyva, A. / Sogues, A. / Megrian, D. / Rodriguez, A. / Gaday, Q. / Ben Assaya, M. / Portela, M. / Haouz, A. / Ducret, A. / Grangeasse, C. / Alzari, P.M. / Dur N, R. / Wehenkel, A.
History
DepositionDec 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Molybdopterin molybdenumtransferase
B: Molybdopterin molybdenumtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6985
Polymers88,4602
Non-polymers2383
Water7,638424
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.443, 94.443, 230.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Molybdopterin molybdenumtransferase


Mass: 44229.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: Cgl0883 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NS03
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris pH 8.5, 30% v/v PEG400, 200 mM Na3Cit

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.14→49.2 Å / Num. obs: 58764 / % possible obs: 99.7 % / Redundancy: 26.4 % / CC1/2: 1 / Rpim(I) all: 0.023 / Net I/σ(I): 21.1
Reflection shellResolution: 2.14→2.19 Å / Redundancy: 25 % / Num. unique obs: 4332 / CC1/2: 0.78 / Rpim(I) all: 0.352 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487-000refinement
XDSMar 15, 2019data reduction
Aimless1.11.19data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→49.2 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2267 2970 5.06 %
Rwork0.1995 --
obs0.2009 58649 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5799 0 15 424 6238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035902
X-RAY DIFFRACTIONf_angle_d0.6048013
X-RAY DIFFRACTIONf_dihedral_angle_d8.024868
X-RAY DIFFRACTIONf_chiral_restr0.05949
X-RAY DIFFRACTIONf_plane_restr0.0061060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.170.33141220.29472449X-RAY DIFFRACTION94
2.17-2.210.26551420.26262618X-RAY DIFFRACTION100
2.21-2.250.29491540.24752607X-RAY DIFFRACTION100
2.25-2.290.26111440.24082577X-RAY DIFFRACTION100
2.29-2.340.2611300.2382623X-RAY DIFFRACTION100
2.34-2.390.26621470.2372629X-RAY DIFFRACTION100
2.39-2.440.24241480.23272612X-RAY DIFFRACTION100
2.44-2.510.30251380.252622X-RAY DIFFRACTION100
2.51-2.570.31131690.24812606X-RAY DIFFRACTION100
2.57-2.650.29781400.2322612X-RAY DIFFRACTION100
2.65-2.730.23111280.2162654X-RAY DIFFRACTION100
2.73-2.830.25171500.21072631X-RAY DIFFRACTION100
2.83-2.950.24161460.21512640X-RAY DIFFRACTION100
2.95-3.080.28811280.22062658X-RAY DIFFRACTION100
3.08-3.240.21141380.22172675X-RAY DIFFRACTION100
3.24-3.440.26491300.20932660X-RAY DIFFRACTION100
3.44-3.710.21581200.19272717X-RAY DIFFRACTION100
3.71-4.080.1811530.17652677X-RAY DIFFRACTION100
4.08-4.670.18761450.14532721X-RAY DIFFRACTION100
4.68-5.890.20451620.172755X-RAY DIFFRACTION100
5.89-49.20.191360.18862936X-RAY DIFFRACTION100
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)
10.4726-0.2111-0.46222.96233.41214.7134-0.0284-0.17460.15520.0036-0.22740.3618-0.244-0.06120.32590.37170.00630.00860.3705-0.03640.4372-7.552744.119478.3271
22.5786-0.3190.30592.9229-0.34141.8417-0.01070.23440.0849-0.27380.0606-0.02610.0932-0.0143-0.05350.325-0.00670.03190.3228-0.00910.26853.14018.784346.9422
32.97131.1169-0.04292.7929-1.78614.23940.15820.27020.8363-0.1773-0.3435-0.6907-0.18810.42280.16540.5478-0.12410.18590.69250.07820.965623.195924.53140.8652
40.1097-0.9641-0.81132.82622.48812.4369-0.08780.09530.0047-0.02950.06690.0794-0.02260.0970.00750.3056-0.0187-0.03440.4219-0.0660.480522.4391.75648.1248
52.3912-0.14440.44682.54760.00951.47990.0182-0.2329-0.03590.3411-0.0483-0.00660.0242-0.10930.02960.32230.0299-0.0110.2382-0.04160.2366.381633.155983.1127
64.50750.6013-0.26655.06580.85735.1166-0.17740.46690.072-0.43560.1333-0.16080.04120.16550.06230.352-0.0016-0.01740.28040.02160.29469.856551.333164.0324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 182 )
2X-RAY DIFFRACTION2chain 'A' and (resid 183 through 330 )
3X-RAY DIFFRACTION3chain 'A' and (resid 331 through 417 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 182 )
5X-RAY DIFFRACTION5chain 'B' and (resid 183 through 330 )
6X-RAY DIFFRACTION6chain 'B' and (resid 331 through 416 )

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