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

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Open data

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Basic information

Entry

Database: PDB / ID: 9ev4

Title

Pyruvate:quinone oxidoreductase (PQO) from Corynebacterium glutamicum CS176

Components

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

Keywords

OXIDOREDUCTASE / Pyruvate:quinone oxidoreductase / pyruvate / carbon metabolism

Function / homology

Function and homology information

thiamine pyrophosphate binding / catalytic activity / magnesium ion binding
Similarity search - Function

Biological species

Corynebacterium glutamicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.474 Å

Authors

Da Silva Lameira, C. / Muenssinger, S. / Yang, L. / Eikmanns, B.J. / Bellinzoni, M.

Funding support

France, 1items

Citation

Journal: 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

Deposition	Mar 28, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 7, 2024	Provider: repository / Type: Initial release

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	9ev4.cif.gz	239.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9ev4.ent.gz	186.9 KB	Display	PDB format
PDBx/mmJSON format	9ev4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ev4_validation.pdf.gz	690.1 KB	Display	wwPDB validaton report
Full document	9ev4_full_validation.pdf.gz	693.5 KB	Display
Data in XML	9ev4_validation.xml.gz	26.9 KB	Display
Data in CIF	9ev4_validation.cif.gz	42.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ev/9ev4 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/9ev4	HTTPS FTP

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Related structure data

Related structure data	9ev3SC 9ev5C 9ev6C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#263 - Nov 2021 Acetohydroxyacid Synthase similarity (8) #213 - Sep 2017 Sirtuins similarity (1) #153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1)

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Assembly

Deposited unit

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

hetero molecules

62.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author&software
Evidence: homology, Homotetrameric enzyme
252 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	68.74, 120.022, 157.059
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-795- HOH
2	1	A-868- HOH
3	1	A-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 interest	Y

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Experimental details

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 52.98 %
Crystal grow	Temperature: 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

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: MASSIF-3 / Wavelength: 0.9677 Å

Detector

Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 3, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9677 Å / Relative weight: 1

Reflection

Resolution: 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!
CC_1/2: 0.997 / CC_1/2 anomalous: -0.016 / R_merge(I) obs: 0.1048 / R_pim(I) all: 0.0291 / R_rim(I) all: 0.1088 / AbsDiff over sigma anomalous: 0.719 / B_aniso tensor eigenvalue 1: 20.7017 Å² / B_aniso tensor eigenvalue 2: 18.8999 Å² / B_aniso tensor eigenvalue 3: 0 Å² / B_aniso tensor eigenvector 1 ortho1: 1 / B_aniso tensor eigenvector 1 ortho2: 0 / B_aniso tensor eigenvector 1 ortho3: 0 / B_aniso tensor eigenvector 2 ortho1: 0 / B_aniso tensor eigenvector 2 ortho2: 1 / B_aniso tensor eigenvector 2 ortho3: 0 / B_aniso tensor eigenvector 3 ortho1: 0 / B_aniso tensor eigenvector 3 ortho2: 0 / B_aniso 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 (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. measured obs	Num. unique all	Num. unique obs	CC_1/2	CC_1/2 anomalous	R_pim(I) all	R_rim(I) all	AbsDiff over sigma anomalous	% possible anomalous	% possible ellipsoidal	% possible ellipsoidal anomalous	% possible spherical	% possible spherical anomalous	Redundancy anomalous	% possible all
4.84-62.973	13.66	0.0726	31.07	45269	45269	3315	3315	0.995	0.047	0.0206	0.0756	0.73	99.8	99.8	99.8	99.8	99.8	7.58	99.8
3.814-4.84	14.65	0.0719	31.78	48575	48575	3315	3315	0.997	-0.021	0.0194	0.0745	0.685	100	100	100	100	100	7.77	100
3.32-3.813	14.82	0.0769	29.59	49129	49129	3315	3315	0.996	-0.075	0.0207	0.0797	0.7	100	100	100	100	100	7.79	100
3.01-3.32	13.59	0.0864	25.09	45039	45039	3315	3315	0.996	-0.184	0.024	0.0898	0.705	100	100	100	100	100	7.09	100
2.791-3.01	11.43	0.0971	19.95	37886	37886	3315	3315	0.995	-0.124	0.0296	0.1016	0.756	100	100	100	100	100	5.94	100
2.623-2.791	13.19	0.1123	18.76	43711	43711	3315	3315	0.995	-0.014	0.0321	0.1168	0.768	100	99.9	100	99.9	100	6.84	99.9
2.489-2.623	13.65	0.1303	16.42	45236	45236	3315	3315	0.995	0.011	0.0366	0.1355	0.764	100	100	100	100	100	7.08	100
2.378-2.488	13.94	0.1511	14.36	46204	46204	3315	3315	0.994	-0.124	0.0419	0.1569	0.739	100	100	100	100	100	7.21	100
2.286-2.378	14.07	0.1794	12.31	46643	46643	3315	3315	0.994	0.012	0.0496	0.1863	0.763	100	99.9	100	99.9	100	7.27	99.9
2.206-2.286	14.24	0.205	10.55	47211	47211	3316	3316	0.993	-0.231	0.0562	0.2127	0.739	100	99.9	100	99.9	100	7.34	99.9
2.135-2.206	14.24	0.246	9.22	47208	47208	3315	3315	0.991	-0.032	0.0675	0.2552	0.724	100	100	100	100	100	7.36	100
2.074-2.135	14.35	0.3156	7.58	47569	47569	3315	3315	0.987	-0.072	0.0861	0.3273	0.715	100	100	100	100	100	7.4	100
2.018-2.074	14.36	0.3955	6.28	47616	47616	3315	3315	0.986	-0.046	0.108	0.4101	0.726	100	100	100	100	100	7.4	100
1.968-2.018	14.43	0.486	5.34	47826	47826	3315	3315	0.978	-0.035	0.1325	0.5039	0.722	100	100	100	100	100	7.42	100
1.923-1.968	14.47	0.626	4.27	47968	47968	3315	3315	0.968	-0.021	0.1701	0.649	0.696	99.9	99.9	99.9	99.9	99.9	7.45	99.9
1.877-1.923	14.46	0.7389	3.73	47933	47933	3315	3315	0.949	-0.047	0.201	0.7661	0.682	91.6	90.8	91.6	90.8	91.6	7.4	90.8
1.825-1.877	14.38	0.7891	3.54	47676	47676	3315	3315	0.938	-0.004	0.2152	0.8182	0.69	79.8	79	79.8	71.3	72.2	7.34	79
1.76-1.825	14.12	0.8537	3.31	46821	46821	3315	3315	0.919	-0.02	0.2352	0.8858	0.684	83.7	83.8	83.7	50	50.1	7.23	83.8
1.667-1.76	13.34	0.8972	2.96	44229	44229	3315	3315	0.887	-0.015	0.2544	0.9331	0.693	77.4	78.4	77.4	29.6	29	6.89	78.4
1.474-1.667	11.34	1.058	2.29	37608	37608	3315	3315	0.793	-0.01	0.3249	1.1083	0.709	76.7	78.2	76.7	9.9	9.3	5.92	78.2

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Processing

Software

Name	Version	Classification
autoPROC	1.0.5 20230726	data processing
Aimless	0.7.13	data scaling
BUSTER	2.10.4	refinement
autoPROC		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 9EV3

Resolution: 1.474→21.33 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.957 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.098 / SU R_free Blow DPI: 0.093 / SU R_free Cruickshank DPI: 0.089

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1903	3344	-	RANDOM
R_work	0.1634	-	-	-
obs	0.1647	66252	60.6 %	-

Displacement parameters

B_iso mean: 29.09 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.8194 Å²	0 Å²	0 Å²
2-	-	0.6556 Å²	0 Å²
3-	-	-	-1.475 Å²

Refine analyze

Luzzati coordinate error obs: 0.19 Å

Refinement step

Cycle: LAST / Resolution: 1.474→21.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4121	0	53	621	4795

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.011	4273	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	0.96	5825	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		1944	SINUSOIDAL	2
X-RAY DIFFRACTION	t_gen_planes		750	HARMONIC	5
X-RAY DIFFRACTION	t_it		4273	HARMONIC	10
X-RAY DIFFRACTION	t_chiral_improper_torsion		581	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_ideal_dist_contact		4328	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_omega_torsion	4.03
X-RAY DIFFRACTION	t_other_torsion	2.46

LS refinement shell

Resolution: 1.474→1.58 Å

	R_factor	Num. reflection	% reflection
R_free	0.2855	67	-
R_work	0.2239	-	-
obs	-	-	6.34 %

Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.1744	-0.2541	0.2839	0.8336	-0.0481	2.1844	0.0538	0.1289	0.1352	0.1289	-0.0994	-0.364	0.1352	-0.364	0.0456	-0.0858	-0.0833	0.032	-0.0143	-0.0225	-0.0693	-12.5462	49.4682	18.4951
2	0	-0.0117	0.1363	1.1837	-0.05	1.0977	0.0552	0.0402	0.0944	0.0402	-0.101	-0.243	0.0944	-0.243	0.0458	-0.1387	-0.0396	0.0083	-0.0158	-0.0368	-0.067	-12.648	54.2067	6.9628
3	3.3036	-1.2907	-0.1835	0.9575	0.0783	1.7721	0.0247	0.0456	0.7362	0.0456	-0.0419	-0.0668	0.7362	-0.0668	0.0172	0.1766	-0.046	-0.035	-0.0861	-0.0188	-0.0507	-2.7645	30.7575	1.5756
4	0.7739	0.0312	0.3763	0.7797	-0.3087	2.7391	0.152	-0.0361	0.7462	-0.0361	-0.1452	0.4362	0.7462	0.4362	-0.0068	0.1766	0.1834	-0.0422	0.0111	0.0512	-0.0327	17.1302	28.1443	11.3011
5	1.8986	-0.8991	-0.4732	2.0662	0.0634	0.9302	0.1739	0.2563	0.2778	0.2563	-0.1043	0.5509	0.2778	0.5509	-0.0697	0.1683	0.0676	-0.0995	0.2242	0.1088	-0.002	23.327	34.0841	33.6267
6	1.274	-0.3646	0.0006	0.8556	-0.3212	2.3499	0.0577	0.2534	0.1294	0.2534	-0.0869	0.1016	0.1294	0.1016	0.0293	0.0344	-0.0764	-0.0073	-0.0517	0.0373	-0.0774	2.8742	43.3418	30.4278
7	2.682	-1.6163	0.5606	4.9865	-1.3148	4.7642	-0.1309	0.609	-0.1943	0.609	0.0974	0.4321	-0.1943	0.4321	0.0335	0.25	-0.1051	-0.0303	0.0782	0.0243	-0.0889	6.1161	47.9458	45.3884
8	0.653	-0.3157	0.1268	1.0349	-0.4297	0.6763	0.1444	0.1156	0.2218	0.1156	-0.208	0.4662	0.2218	0.4662	0.0636	0.1095	0.0221	-0.0662	0.163	0.0788	0.026	20.627	40.4907	28.0918

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|3 - 90 }	A	3 - 90
2	X-RAY DIFFRACTION	2	{ A\|91 - 164 }	A	91 - 164
3	X-RAY DIFFRACTION	3	{ A\|165 - 200 }	A	165 - 200
4	X-RAY DIFFRACTION	4	{ A\|201 - 328 }	A	201 - 328
5	X-RAY DIFFRACTION	5	{ A\|329 - 371 }	A	329 - 371
6	X-RAY DIFFRACTION	6	{ A\|372 - 462 }	A	372 - 462
7	X-RAY DIFFRACTION	7	{ A\|463 - 519 }	A	463 - 519
8	X-RAY DIFFRACTION	8	{ A\|520 - 577 }	A	520 - 577

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