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- PDB-4igh: High resolution crystal structure of human dihydroorotate dehydro... -

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Basic information

Entry
Database: PDB / ID: 4igh
TitleHigh resolution crystal structure of human dihydroorotate dehydrogenase bound with 4-quinoline carboxylic acid analog
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrialDihydroorotate dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / anti-viral / quinoline-4-carboxylic acid / redox / dehydrogenase / FMN / membrane / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane ...pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane / mitochondrion / nucleoplasm / cytosol
Similarity search - Function
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
Chem-1EA / FLAVIN MONONUCLEOTIDE / OROTIC ACID / 3-[decyl(dimethyl)ammonio]propane-1-sulfonate / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDeng, X. / Das, P. / Fontoura, B.M.A. / Phillips, M.A. / De Brabander, J.K.
CitationJournal: ACS MED.CHEM.LETT. / Year: 2013
Title: SAR Based Optimization of a 4-Quinoline Carboxylic Acid Analog with Potent Anti-Viral Activity.
Authors: Das, P. / Deng, X. / Zhang, L. / Roth, M.G. / Fontoura, B.M. / Phillips, M.A. / De Brabander, J.K.
History
DepositionDec 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1447
Polymers40,6241
Non-polymers1,5206
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.786, 90.786, 122.485
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydroorotate dehydrogenase (quinone), mitochondrial / Dihydroorotate dehydrogenase (quinone) / DHOdehase / Dihydroorotate oxidase


Mass: 40624.301 Da / Num. of mol.: 1 / Fragment: UNP residues 32-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone)

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Non-polymers , 6 types, 303 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ORO / OROTIC ACID / Orotic acid


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical ChemComp-1EA / 6-fluoro-2-[2-methyl-4-phenoxy-5-(propan-2-yl)phenyl]quinoline-4-carboxylic acid


Mass: 415.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H22FNO3
#5: Chemical ChemComp-ZWI / 3-[decyl(dimethyl)ammonio]propane-1-sulfonate


Mass: 307.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H33NO3S
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 1.72 M ammonium sulfate, 0.1 M sodium acetate, pH 5.4, 1.5 M sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2012
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.22→78.62 Å / Num. all: 172407 / Num. obs: 171829 / % possible obs: 99.66 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 27
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 7 % / Rmerge(I) obs: 0.937 / Mean I/σ(I) obs: 2 / Num. unique all: 8552 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D3G

1d3g


Resolution: 1.3→78.62 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.973 / SU ML: 0.017 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.032 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14764 4304 3 %RANDOM
Rwork0.13761 ---
obs0.13791 171829 99.53 %-
all-172407 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å20 Å2
2--0.23 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.3→78.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 105 297 3121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0193111
X-RAY DIFFRACTIONr_bond_other_d0.0060.022220
X-RAY DIFFRACTIONr_angle_refined_deg2.5832.024237
X-RAY DIFFRACTIONr_angle_other_deg1.39435378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4625401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48222.92137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00815538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6271535
X-RAY DIFFRACTIONr_chiral_restr0.2330.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0213540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02648
X-RAY DIFFRACTIONr_rigid_bond_restr10.16235330
X-RAY DIFFRACTIONr_sphericity_free77.794581
X-RAY DIFFRACTIONr_sphericity_bonded18.10755483
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 291 -
Rwork0.189 9771 -
obs-8542 99.91 %
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)
13.7117-3.35511.943818.9448-4.68517.61660.1530.4761-0.4707-1.09780.01290.55770.9434-0.2472-0.16590.2998-0.0535-0.03650.2796-0.0640.2149-5.53825.8346-9.1168
23.94662.1197-0.45294.555-1.60794.50560.04270.0519-0.1245-0.18890.04130.2250.3132-0.3737-0.0840.0559-0.0025-0.02890.1499-0.01420.0877-11.023836.1429-1.2218
32.39690.5641-0.24538.50121.20014.9242-0.0177-0.2187-0.22380.1674-0.06850.2250.5216-0.14150.08630.1210.01250.05180.11150.04540.12030.172821.67119.2892
40.7556-0.0253-0.58160.3209-0.02770.90890.04350.05560.0361-0.0323-0.02820.0692-0.0243-0.1258-0.01530.01830.0131-0.00610.0667-0.00160.0444-4.678441.71147.5767
510.8581-6.6044-2.23849.04010.5581.6521-0.2149-0.2521-0.59210.26690.11060.57770.226-0.14630.10430.0569-0.02110.03940.10110.00930.0964-10.680628.860622.2428
61.4574-0.2216-0.4971.20120.04292.00460.0795-0.04350.2122-0.0221-0.0326-0.065-0.20190.1103-0.04690.02440.00120.01150.0722-0.01220.0466-0.473447.918819.3266
71.9201-0.252-1.17410.29270.42531.40280.028-0.15410.1859-0.00880.0379-0.0425-0.08070.1706-0.0660.04080.003-0.00560.0917-0.00170.06739.731645.139822.4818
80.5528-0.16320.00570.5492-0.18391.13860.0069-0.06630.03210.0118-0.0028-0.0355-0.01390.0853-0.00410.00660.00810.00220.0421-0.00120.027714.095238.48236.9017
91.4954-0.3561-0.431.5265-0.07310.96620.00480.055-0.0998-0.0542-0.01260.08710.1382-0.02720.00780.03220.00840.00920.04010.00270.03626.517728.08596.7604
101.70421.10361.44723.44080.5943.09310.086-0.0752-0.40960.11510.01-0.13530.40250.0594-0.0960.12990.04330.0320.07370.02920.157412.04117.782912.4744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 46
2X-RAY DIFFRACTION2A47 - 70
3X-RAY DIFFRACTION3A74 - 89
4X-RAY DIFFRACTION4A90 - 165
5X-RAY DIFFRACTION5A166 - 176
6X-RAY DIFFRACTION6A177 - 213
7X-RAY DIFFRACTION7A214 - 272
8X-RAY DIFFRACTION8A273 - 326
9X-RAY DIFFRACTION9A327 - 371
10X-RAY DIFFRACTION10A372 - 395

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