PDB-6b8s: Crystal Structure of Dihydroorotate Dehydrogenase from Helicobact...

ID or keywords:

Entry

Database: PDB / ID: 6b8s

Title

Crystal Structure of Dihydroorotate Dehydrogenase from Helicobacter pylori with bound FMN

Components

Dihydroorotate dehydrogenase (quinone)

Keywords

OXIDOREDUCTASE / SSGCID / dihydroorotate dehydrogenase / Helicobacter pylori / FMN / flavin mononucleotide / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.25 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of Dihydroorotate Dehydrogenase from Helicobacter pylori with bound FMN
Authors: Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Oct 9, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 15, 2020	Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6b8s.cif.gz	274 KB	Display	PDBx/mmCIF format
PDB format	pdb6b8s.ent.gz	218.1 KB	Display	PDB format
PDBx/mmJSON format	6b8s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6b8s_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	6b8s_full_validation.pdf.gz	1 MB	Display
Data in XML	6b8s_validation.xml.gz	26.2 KB	Display
Data in CIF	6b8s_validation.cif.gz	36 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b8/6b8s ftp://data.pdbj.org/pub/pdb/validation_reports/b8/6b8s	HTTPS FTP

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Related structure data

Related structure data	1f76S S: Starting model for refinement
Similar structure data	2bvw-2 1oc6-d 2fqi-d 2wv8-d 1qjw-2 2htr-d 1oc5-d 4ax7-1 2hv6-2 3kvm-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-HepyC.00487.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Dihydroorotate dehydrogenase (quinone)

B: Dihydroorotate dehydrogenase (quinone)

hetero molecules

81.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Dihydroorotate dehydrogenase (quinone)

hetero molecules

defined by author
Evidence: gel filtration
40.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Dihydroorotate dehydrogenase (quinone)

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.440, 69.080, 100.100
Angle α, β, γ (deg.)	90.000, 98.060, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Dihydroorotate dehydrogenase (quinone) / DHOdehase / DHODase / Dihydroorotate oxidase Mass: 40064.199 Da / Num. of mol.: 2 / Fragment: HepyC.00487.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria) Strain: G27 / Gene: pyrD, HPG27_417 / Plasmid: HepyC.00487.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B5Z6I2, dihydroorotate dehydrogenase (quinone)
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.77 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: HepyC.00487.a.B1.PW38289 at 18.5 mg/ml was mixed 1:1 with MCSG1(d3): 0.2 M magnesium chloride, 0.1 M Tris:HCl, pH=8.5, 30% (v/v) PEG-400 . Tray: 293601d3, puck: xyo1-6.

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2017 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.25→48.952 Å / Num. obs: 31777 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.803 % / B_iso Wilson estimate: 47.59 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.043 / R_rim(I) all: 0.051 / Χ²: 1.022 / Net I/σ(I): 17.87 / Num. measured all: 120853 / Scaling rejects: 4

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.25-2.31	3.833	0.562	2.42	8930	2330	2330	0.784	0.654	100
2.31-2.37	3.826	0.411	3.21	8766	2296	2291	0.853	0.479	99.8
2.37-2.44	3.838	0.306	4.25	8437	2195	2198	0.931	0.356	100
2.44-2.52	3.82	0.248	5.27	8256	2162	2161	0.947	0.289	100
2.52-2.6	3.833	0.202	6.36	8008	2088	2089	0.961	0.235	100
2.6-2.69	3.832	0.156	8.17	7714	2017	2013	0.978	0.182	99.8
2.69-2.79	3.824	0.116	10.89	7506	1968	1963	0.986	0.135	99.7
2.79-2.9	3.832	0.097	13.07	7257	1895	1894	0.99	0.113	99.9
2.9-3.03	3.822	0.073	16.54	6891	1809	1803	0.994	0.085	99.7
3.03-3.18	3.823	0.056	20.95	6533	1714	1709	0.996	0.066	99.7
3.18-3.35	3.808	0.044	25.12	6249	1651	1641	0.998	0.052	99.4
3.35-3.56	3.813	0.038	28.81	5986	1577	1570	0.998	0.044	99.6
3.56-3.8	3.782	0.035	31.38	5545	1470	1466	0.998	0.041	99.7
3.8-4.11	3.781	0.03	35.76	5116	1354	1353	0.998	0.035	99.9
4.11-4.5	3.779	0.029	38.23	4788	1277	1267	0.998	0.034	99.2
4.5-5.03	3.769	0.027	39.89	4282	1143	1136	0.999	0.032	99.4
5.03-5.81	3.739	0.027	40.01	3702	993	990	0.999	0.031	99.7
5.81-7.12	3.679	0.029	39.06	3193	878	868	0.999	0.034	98.9
7.12-10.06	3.667	0.028	42.97	2442	670	666	0.998	0.033	99.4
10.06-48.952	3.393	0.026	42.94	1252	380	369	0.998	0.032	97.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1F76

1f76

Resolution: 2.25→48.952 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.66

	R_factor	Num. reflection	% reflection
R_free	0.2393	1983	6.24 %
R_work	0.1816	-	-
obs	0.1851	31767	99.69 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 128.85 Å² / B_iso mean: 57.8575 Å² / B_iso min: 21.02 Å²

Refinement step

Cycle: final / Resolution: 2.25→48.952 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4956	0	82	118	5156
B_iso mean	-	-	44.67	49.67	-
Num. residues	-	-	-	-	671

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.25-2.3063	0.3451	125	0.269	2121	2246	100
2.3063-2.3686	0.3051	153	0.237	2119	2272	100
2.3686-2.4383	0.2814	141	0.2235	2093	2234	100
2.4383-2.517	0.2923	153	0.2121	2112	2265	100
2.517-2.607	0.2986	129	0.213	2132	2261	100
2.607-2.7114	0.3163	131	0.2053	2127	2258	100
2.7114-2.8348	0.2774	147	0.2075	2123	2270	100
2.8348-2.9842	0.2566	147	0.2019	2115	2262	100
2.9842-3.1711	0.2637	152	0.1892	2120	2272	100
3.1711-3.4159	0.2446	152	0.1886	2113	2265	100
3.4159-3.7596	0.2083	126	0.1721	2140	2266	100
3.7596-4.3033	0.2542	126	0.1529	2161	2287	100
4.3033-5.4206	0.1906	149	0.1519	2131	2280	100
5.4206-48.9638	0.212	152	0.1832	2177	2329	99

Refinement TLS params.

Method: refined / 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	2.7501	-0.3118	-1.3241	3.4324	-1.5981	2.5729	0.1446	-0.2905	-0.6119	-0.1964	-0.0771	-0.5626	0.5312	0.0231	-0.0637	0.3402	-0.0618	0.0211	0.466	0.1066	0.3477	5.7026	-17.4799	21.6564
2	3.1772	0.6437	0.7412	3.1999	-0.9821	3.9494	-0.1325	-0.2451	0.2356	-0.2988	0.2038	0.2809	0.0002	-0.3154	0.0203	0.3029	-0.0357	-0.0505	0.337	0.0526	0.3032	0.1233	-5.5951	12.535
3	3.1833	0.0402	0.9566	3.9937	-0.7042	4.4104	-0.052	-0.0872	-0.1028	-0.5546	-0.0172	0.0405	0.4483	-0.066	0.2195	0.4345	-0.0718	0.01	0.2447	0.0317	0.2961	6.3016	-10.528	9.3265
4	2.1972	-0.216	0.5213	7.1431	-3.0011	6.6249	-0.5494	0.6182	-0.0222	-1.5012	-0.2274	-0.6154	0.6348	0.6167	0.1202	1.3088	-0.2391	0.1244	0.5852	-0.0084	0.301	11.7614	-8.8858	-8.5491
5	2.8175	-1.8384	-1.5286	2.9453	-1.2866	4.9033	-0.3678	1.2289	0.6639	-1.4952	0.1854	-0.0681	-0.1553	0.1581	0.065	0.9485	-0.231	-0.0421	0.6622	0.1463	0.4073	7.445	0.3597	-4.9708
6	2.0032	-1.4825	-0.2078	2.4576	-0.8403	3.7782	-0.5137	0.515	0.6802	-1.092	0.2231	-0.2817	-0.5246	0.4863	0.3112	0.8181	-0.1791	-0.0812	0.4954	0.184	0.5161	13.1816	6.8188	-0.3473
7	4.5143	-1.0649	1.7876	5.3583	-3.3395	4.9089	-0.2657	-0.191	-0.0397	0.2665	-0.7416	-1.1216	0.3199	1.1461	0.5707	0.4118	0.0443	0.0399	0.9136	0.18	0.5519	25.4496	-5.6694	14.8759
8	3.1339	0.483	-0.267	3.8859	-1.4776	4.0142	-0.1545	-0.0982	0.4235	-0.0415	-0.051	-0.1123	-0.6866	0.3732	0.2523	0.4055	-0.0855	-0.096	0.3213	0.0025	0.3726	12.1224	6.5422	15.2123
9	2.9779	0.2922	-0.0951	5.0652	-0.1507	4.0801	-0.1325	-0.7576	0.8568	0.7137	0.0113	0.6555	-0.8509	-0.8013	-0.126	0.453	0.1872	-0.0768	0.4758	-0.2053	0.6505	0.6897	10.7227	23.0347
10	2.9799	-0.5987	0.318	2.9895	1.693	3.4423	-0.009	-0.4048	-0.077	0.5031	0.1159	0.0087	0.1419	0.3574	-0.1094	0.3287	0.0745	0.0726	0.4391	-0.0682	0.4238	17.6781	13.6096	-25.1384
11	3.6453	-1.2439	-0.049	2.4558	0.6462	2.5045	-0.0429	-0.0114	-0.4009	0.1993	-0.0421	0.4017	0.0981	-0.1761	0.0994	0.3357	0.0096	0.1086	0.4245	-0.0525	0.5476	15.5132	4.011	-34.7165
12	4.3525	-0.3997	-0.5089	4.2543	0.048	6.5772	-0.3783	0.2247	-1.1142	0.7582	0.2102	0.7759	1.073	-0.0212	0.1106	0.5824	-0.0202	0.1287	0.4266	-0.041	0.977	17.4078	-12.7792	-34.1589
13	3.4365	-1.6819	-0.0739	3.8961	0.64	3.5457	-0.1601	0.3906	-0.6653	-0.2465	0.0778	0.1121	0.2303	0.3324	-0.0387	0.3789	0.0988	-0.0022	0.5161	-0.1671	0.6788	28.385	-6.4866	-43.3449
14	3.6954	-1.0958	0.2541	3.6336	-0.5852	2.5258	0.29	0.6659	-0.1401	-0.5736	-0.2948	0.1306	0.0135	-0.0069	-0.0116	0.3105	0.0557	-0.0039	0.6048	-0.1083	0.3942	20.5394	6.816	-49.4864

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 31 )	A	2 - 31
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 104 )	A	32 - 104
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 105 through 146 )	A	105 - 146
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 147 through 167 )	A	147 - 167
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 168 through 204 )	A	168 - 204
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 205 through 241 )	A	205 - 241
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 242 through 258 )	A	242 - 258
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 259 through 319 )	A	259 - 319
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 320 through 348 )	A	320 - 348
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2 through 31 )	B	2 - 31
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 32 through 123 )	B	32 - 123
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 124 through 204 )	B	124 - 204
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 205 through 258 )	B	205 - 258
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 259 through 348 )	B	259 - 348

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