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- PDB-9ev4: Pyruvate:quinone oxidoreductase (PQO) from Corynebacterium glutam... -

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Basic information

Entry
Database: PDB / ID: 9ev4
TitlePyruvate:quinone oxidoreductase (PQO) from Corynebacterium glutamicum CS176
ComponentsThiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
KeywordsOXIDOREDUCTASE / Pyruvate:quinone oxidoreductase / pyruvate / carbon metabolism
Function / homology
Function and homology information


thiamine pyrophosphate binding / catalytic activity / magnesium ion binding
Similarity search - Function
: / : / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.474 Å
AuthorsDa Silva Lameira, C. / Muenssinger, S. / Yang, L. / Eikmanns, B.J. / Bellinzoni, M.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE92-0003 France
CitationJournal: Febs J. / Year: 2024
Title: Corynebacterium glutamicum pyruvate:quinone oxidoreductase: an enigmatic metabolic enzyme with unusual structural features.
Authors: da Silva Lameira, C. / Munssinger, S. / Yang, L. / Eikmanns, B.J. / Bellinzoni, M.
History
DepositionMar 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9042
Polymers62,1181
Non-polymers7861
Water11,187621
1
A: Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
hetero molecules

A: Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
hetero molecules

A: Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
hetero molecules

A: Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,6158
Polymers248,4734
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area25560 Å2
ΔGint-133 kcal/mol
Surface area67220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.74, 120.022, 157.059
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-795-

HOH

21A-868-

HOH

31A-1284-

HOH

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Components

#1: Protein Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] / pyruvate:quinone oxidoreductase


Mass: 62118.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: CS176 / Gene: Cgl2610 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8NMG5, pyruvate dehydrogenase (quinone)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25 % (w/v) PEG 4000, 8 % (v/v) isopropanol, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.474→62.973 Å / Num. obs: 66301 / % possible obs: 94.7 % / Redundancy: 13.84 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.997 / CC1/2 anomalous: -0.016 / Rmerge(I) obs: 0.1048 / Rpim(I) all: 0.0291 / Rrim(I) all: 0.1088 / AbsDiff over sigma anomalous: 0.719 / Baniso tensor eigenvalue 1: 20.7017 Å2 / Baniso tensor eigenvalue 2: 18.8999 Å2 / Baniso tensor eigenvalue 3: 0 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 1.843 Å / Aniso diffraction limit 2: 1.861 Å / Aniso diffraction limit 3: 1.473 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 12.92 / Num. measured all: 917357 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 94.6 / % possible ellipsoidal: 94.7 / % possible ellipsoidal anomalous: 94.6 / % possible spherical: 60.6 / % possible spherical anomalous: 59.7 / Redundancy anomalous: 7.19 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
4.84-62.97313.660.072631.074526945269331533150.9950.0470.02060.07560.7399.899.899.899.899.87.5899.8
3.814-4.8414.650.071931.784857548575331533150.997-0.0210.01940.07450.6851001001001001007.77100
3.32-3.81314.820.076929.594912949129331533150.996-0.0750.02070.07970.71001001001001007.79100
3.01-3.3213.590.086425.094503945039331533150.996-0.1840.0240.08980.7051001001001001007.09100
2.791-3.0111.430.097119.953788637886331533150.995-0.1240.02960.10160.7561001001001001005.94100
2.623-2.79113.190.112318.764371143711331533150.995-0.0140.03210.11680.76810099.910099.91006.8499.9
2.489-2.62313.650.130316.424523645236331533150.9950.0110.03660.13550.7641001001001001007.08100
2.378-2.48813.940.151114.364620446204331533150.994-0.1240.04190.15690.7391001001001001007.21100
2.286-2.37814.070.179412.314664346643331533150.9940.0120.04960.18630.76310099.910099.91007.2799.9
2.206-2.28614.240.20510.554721147211331633160.993-0.2310.05620.21270.73910099.910099.91007.3499.9
2.135-2.20614.240.2469.224720847208331533150.991-0.0320.06750.25520.7241001001001001007.36100
2.074-2.13514.350.31567.584756947569331533150.987-0.0720.08610.32730.7151001001001001007.4100
2.018-2.07414.360.39556.284761647616331533150.986-0.0460.1080.41010.7261001001001001007.4100
1.968-2.01814.430.4865.344782647826331533150.978-0.0350.13250.50390.7221001001001001007.42100
1.923-1.96814.470.6264.274796847968331533150.968-0.0210.17010.6490.69699.999.999.999.999.97.4599.9
1.877-1.92314.460.73893.734793347933331533150.949-0.0470.2010.76610.68291.690.891.690.891.67.490.8
1.825-1.87714.380.78913.544767647676331533150.938-0.0040.21520.81820.6979.87979.871.372.27.3479
1.76-1.82514.120.85373.314682146821331533150.919-0.020.23520.88580.68483.783.883.75050.17.2383.8
1.667-1.7613.340.89722.964422944229331533150.887-0.0150.25440.93310.69377.478.477.429.6296.8978.4
1.474-1.66711.341.0582.293760837608331533150.793-0.010.32491.10830.70976.778.276.79.99.35.9278.2

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Processing

Software
NameVersionClassification
autoPROC1.0.5 20230726data processing
Aimless0.7.13data scaling
BUSTER2.10.4refinement
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9EV3

9ev3


Resolution: 1.474→21.33 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.098 / SU Rfree Blow DPI: 0.093 / SU Rfree Cruickshank DPI: 0.089
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 3344 -RANDOM
Rwork0.1634 ---
obs0.1647 66252 60.6 %-
Displacement parametersBiso mean: 29.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.8194 Å20 Å20 Å2
2--0.6556 Å20 Å2
3----1.475 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.474→21.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4121 0 53 621 4795
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114273HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.965825HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1944SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes750HARMONIC5
X-RAY DIFFRACTIONt_it4273HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion581SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4328SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.03
X-RAY DIFFRACTIONt_other_torsion2.46
LS refinement shellResolution: 1.474→1.58 Å
RfactorNum. reflection% reflection
Rfree0.2855 67 -
Rwork0.2239 --
obs--6.34 %
Refinement TLS params.

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)
11.1744-0.25410.28390.8336-0.04812.18440.05380.12890.13520.1289-0.0994-0.3640.1352-0.3640.0456-0.0858-0.08330.032-0.0143-0.0225-0.0693-12.546249.468218.4951
20-0.01170.13631.1837-0.051.09770.05520.04020.09440.0402-0.101-0.2430.0944-0.2430.0458-0.1387-0.03960.0083-0.0158-0.0368-0.067-12.64854.20676.9628
33.3036-1.2907-0.18350.95750.07831.77210.02470.04560.73620.0456-0.0419-0.06680.7362-0.06680.01720.1766-0.046-0.035-0.0861-0.0188-0.0507-2.764530.75751.5756
40.77390.03120.37630.7797-0.30872.73910.152-0.03610.7462-0.0361-0.14520.43620.74620.4362-0.00680.17660.1834-0.04220.01110.0512-0.032717.130228.144311.3011
51.8986-0.8991-0.47322.06620.06340.93020.17390.25630.27780.2563-0.10430.55090.27780.5509-0.06970.16830.0676-0.09950.22420.1088-0.00223.32734.084133.6267
61.274-0.36460.00060.8556-0.32122.34990.05770.25340.12940.2534-0.08690.10160.12940.10160.02930.0344-0.0764-0.0073-0.05170.0373-0.07742.874243.341830.4278
72.682-1.61630.56064.9865-1.31484.7642-0.13090.609-0.19430.6090.09740.4321-0.19430.43210.03350.25-0.1051-0.03030.07820.0243-0.08896.116147.945845.3884
80.653-0.31570.12681.0349-0.42970.67630.14440.11560.22180.1156-0.2080.46620.22180.46620.06360.10950.0221-0.06620.1630.07880.02620.62740.490728.0918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - 90 }A3 - 90
2X-RAY DIFFRACTION2{ A|91 - 164 }A91 - 164
3X-RAY DIFFRACTION3{ A|165 - 200 }A165 - 200
4X-RAY DIFFRACTION4{ A|201 - 328 }A201 - 328
5X-RAY DIFFRACTION5{ A|329 - 371 }A329 - 371
6X-RAY DIFFRACTION6{ A|372 - 462 }A372 - 462
7X-RAY DIFFRACTION7{ A|463 - 519 }A463 - 519
8X-RAY DIFFRACTION8{ A|520 - 577 }A520 - 577

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