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

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Basic information

Entry
Database: PDB / ID: 6b8s
TitleCrystal Structure of Dihydroorotate Dehydrogenase from Helicobacter pylori with bound FMN
ComponentsDihydroorotate dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE / 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 (quinone) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel ...Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / TRIETHYLENE GLYCOL / Dihydroorotate dehydrogenase (quinone)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Crystal structure of di­hydroorotate de­hydrogenase from Helicobacter pylori with bound flavin mononucleotide
Authors: Agarwal, A.A. / Georgiades, J.D. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E. / Barrett, K.F. / Craig, J.K. / Van Voorhis, W.C. / Myler, P.J. / Smith, C.L.
History
DepositionOct 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Oct 4, 2023Group: 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
Revision 1.3Mar 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (quinone)
B: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3416
Polymers80,1282
Non-polymers1,2134
Water2,090116
1
A: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6713
Polymers40,0641
Non-polymers6072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6713
Polymers40,0641
Non-polymers6072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 number4
Space group name H-MP1211

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Components

#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
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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→48.952 Å / Num. obs: 31777 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.803 % / Biso Wilson estimate: 47.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(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 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.313.8330.5622.428930233023300.7840.654100
2.31-2.373.8260.4113.218766229622910.8530.47999.8
2.37-2.443.8380.3064.258437219521980.9310.356100
2.44-2.523.820.2485.278256216221610.9470.289100
2.52-2.63.8330.2026.368008208820890.9610.235100
2.6-2.693.8320.1568.177714201720130.9780.18299.8
2.69-2.793.8240.11610.897506196819630.9860.13599.7
2.79-2.93.8320.09713.077257189518940.990.11399.9
2.9-3.033.8220.07316.546891180918030.9940.08599.7
3.03-3.183.8230.05620.956533171417090.9960.06699.7
3.18-3.353.8080.04425.126249165116410.9980.05299.4
3.35-3.563.8130.03828.815986157715700.9980.04499.6
3.56-3.83.7820.03531.385545147014660.9980.04199.7
3.8-4.113.7810.0335.765116135413530.9980.03599.9
4.11-4.53.7790.02938.234788127712670.9980.03499.2
4.5-5.033.7690.02739.894282114311360.9990.03299.4
5.03-5.813.7390.02740.0137029939900.9990.03199.7
5.81-7.123.6790.02939.0631938788680.9990.03498.9
7.12-10.063.6670.02842.9724426706660.9980.03399.4
10.06-48.9523.3930.02642.9412523803690.9980.03297.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2393 1983 6.24 %
Rwork0.1816 --
obs0.1851 31767 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.85 Å2 / Biso mean: 57.8575 Å2 / Biso min: 21.02 Å2
Refinement stepCycle: final / Resolution: 2.25→48.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4956 0 82 118 5156
Biso mean--44.67 49.67 -
Num. residues----671
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.30630.34511250.26921212246100
2.3063-2.36860.30511530.23721192272100
2.3686-2.43830.28141410.223520932234100
2.4383-2.5170.29231530.212121122265100
2.517-2.6070.29861290.21321322261100
2.607-2.71140.31631310.205321272258100
2.7114-2.83480.27741470.207521232270100
2.8348-2.98420.25661470.201921152262100
2.9842-3.17110.26371520.189221202272100
3.1711-3.41590.24461520.188621132265100
3.4159-3.75960.20831260.172121402266100
3.7596-4.30330.25421260.152921612287100
4.3033-5.42060.19061490.151921312280100
5.4206-48.96380.2121520.18322177232999
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)
12.7501-0.3118-1.32413.4324-1.59812.57290.1446-0.2905-0.6119-0.1964-0.0771-0.56260.53120.0231-0.06370.3402-0.06180.02110.4660.10660.34775.7026-17.479921.6564
23.17720.64370.74123.1999-0.98213.9494-0.1325-0.24510.2356-0.29880.20380.28090.0002-0.31540.02030.3029-0.0357-0.05050.3370.05260.30320.1233-5.595112.535
33.18330.04020.95663.9937-0.70424.4104-0.052-0.0872-0.1028-0.5546-0.01720.04050.4483-0.0660.21950.4345-0.07180.010.24470.03170.29616.3016-10.5289.3265
42.1972-0.2160.52137.1431-3.00116.6249-0.54940.6182-0.0222-1.5012-0.2274-0.61540.63480.61670.12021.3088-0.23910.12440.5852-0.00840.30111.7614-8.8858-8.5491
52.8175-1.8384-1.52862.9453-1.28664.9033-0.36781.22890.6639-1.49520.1854-0.0681-0.15530.15810.0650.9485-0.231-0.04210.66220.14630.40737.4450.3597-4.9708
62.0032-1.4825-0.20782.4576-0.84033.7782-0.51370.5150.6802-1.0920.2231-0.2817-0.52460.48630.31120.8181-0.1791-0.08120.49540.1840.516113.18166.8188-0.3473
74.5143-1.06491.78765.3583-3.33954.9089-0.2657-0.191-0.03970.2665-0.7416-1.12160.31991.14610.57070.41180.04430.03990.91360.180.551925.4496-5.669414.8759
83.13390.483-0.2673.8859-1.47764.0142-0.1545-0.09820.4235-0.0415-0.051-0.1123-0.68660.37320.25230.4055-0.0855-0.0960.32130.00250.372612.12246.542215.2123
92.97790.2922-0.09515.0652-0.15074.0801-0.1325-0.75760.85680.71370.01130.6555-0.8509-0.8013-0.1260.4530.1872-0.07680.4758-0.20530.65050.689710.722723.0347
102.9799-0.59870.3182.98951.6933.4423-0.009-0.4048-0.0770.50310.11590.00870.14190.3574-0.10940.32870.07450.07260.4391-0.06820.423817.678113.6096-25.1384
113.6453-1.2439-0.0492.45580.64622.5045-0.0429-0.0114-0.40090.1993-0.04210.40170.0981-0.17610.09940.33570.00960.10860.4245-0.05250.547615.51324.011-34.7165
124.3525-0.3997-0.50894.25430.0486.5772-0.37830.2247-1.11420.75820.21020.77591.073-0.02120.11060.5824-0.02020.12870.4266-0.0410.97717.4078-12.7792-34.1589
133.4365-1.6819-0.07393.89610.643.5457-0.16010.3906-0.6653-0.24650.07780.11210.23030.3324-0.03870.37890.0988-0.00220.5161-0.16710.678828.385-6.4866-43.3449
143.6954-1.09580.25413.6336-0.58522.52580.290.6659-0.1401-0.5736-0.29480.13060.0135-0.0069-0.01160.31050.0557-0.00390.6048-0.10830.394220.53946.816-49.4864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 31 )A2 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 104 )A32 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 146 )A105 - 146
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 167 )A147 - 167
5X-RAY DIFFRACTION5chain 'A' and (resid 168 through 204 )A168 - 204
6X-RAY DIFFRACTION6chain 'A' and (resid 205 through 241 )A205 - 241
7X-RAY DIFFRACTION7chain 'A' and (resid 242 through 258 )A242 - 258
8X-RAY DIFFRACTION8chain 'A' and (resid 259 through 319 )A259 - 319
9X-RAY DIFFRACTION9chain 'A' and (resid 320 through 348 )A320 - 348
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 31 )B2 - 31
11X-RAY DIFFRACTION11chain 'B' and (resid 32 through 123 )B32 - 123
12X-RAY DIFFRACTION12chain 'B' and (resid 124 through 204 )B124 - 204
13X-RAY DIFFRACTION13chain 'B' and (resid 205 through 258 )B205 - 258
14X-RAY DIFFRACTION14chain 'B' and (resid 259 through 348 )B259 - 348

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