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- PDB-4js3: Crystal structure of human dihydroorotate dehydrogenase (DHODH) w... -

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Basic information

Entry
Database: PDB / ID: 4js3
TitleCrystal structure of human dihydroorotate dehydrogenase (DHODH) with 057
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrial
KeywordsOXIDOREDUCTASE / FMN binding / mitochondrion inner membrane
Function / homology
Function and homology information


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / 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) / dihydroorotate dehydrogenase (quinone) activity / 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 ...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
ACETIC ACID / FLAVIN MONONUCLEOTIDE / Chem-JS3 / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhu, L. / Li, H. / Zhu, J. / Ren, X.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of human dihydroorotate dehydrogenase (DHODH) with 057
Authors: Zhu, L. / Li, H. / Zhu, J. / Ren, X.
History
DepositionMar 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,52416
Polymers42,6361
Non-polymers1,88815
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.820, 90.820, 123.300
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 / DHOdehase / Dihydroorotate oxidase


Mass: 42636.414 Da / Num. of mol.: 1 / Fragment: UNP residues 29-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Production host: Escherichia coli (E. coli)
References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone)

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Non-polymers , 6 types, 279 molecules

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


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


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical ChemComp-JS3 / 2-chloro-4-methyl-N-(naphthalen-2-yl)-1,3-thiazole-5-carboxamide


Mass: 302.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11ClN2OS
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsEXPRESSION TAG LISTED IN SEQADV CAN NOT BE SEEN IN THE CRYSTAL STRUCTURE.

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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: 3.44 Å3/Da / Density % sol: 64.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M acetate pH 4.8, 40mM UDAO, 20.8mM N,N-dimethyldecylamine-N-oxide(DDAO), 2mM DHO, 2.4-2.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 9, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2→29.728 Å / Num. all: 40294 / Num. obs: 40137 / % possible obs: 99.61 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.05 Å / % possible all: 99.74

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1d3g

1d3g


Resolution: 2→29.728 Å / SU ML: 0.13 / σ(F): 0.49 / Phase error: 14.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1787 2012 5.01 %RANDOM
Rwork0.1502 ---
obs0.1516 40137 99.61 %-
all-40294 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 117 264 3173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072997
X-RAY DIFFRACTIONf_angle_d1.3584066
X-RAY DIFFRACTIONf_dihedral_angle_d14.3341112
X-RAY DIFFRACTIONf_chiral_restr0.071443
X-RAY DIFFRACTIONf_plane_restr0.006530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05020.19461410.15512683X-RAY DIFFRACTION100
2.0502-2.10560.20031290.15392707X-RAY DIFFRACTION100
2.1056-2.16760.1941420.14942706X-RAY DIFFRACTION100
2.1676-2.23750.17671290.14422695X-RAY DIFFRACTION100
2.2375-2.31750.18311390.14372705X-RAY DIFFRACTION100
2.3175-2.41020.18141740.14522696X-RAY DIFFRACTION100
2.4102-2.51980.18031490.15082694X-RAY DIFFRACTION100
2.5198-2.65260.18391500.15082676X-RAY DIFFRACTION100
2.6526-2.81870.19061240.14972756X-RAY DIFFRACTION100
2.8187-3.03610.18011440.14412722X-RAY DIFFRACTION100
3.0361-3.34130.19171530.14032737X-RAY DIFFRACTION100
3.3413-3.82390.14771600.13712724X-RAY DIFFRACTION100
3.8239-4.81440.16361310.13972782X-RAY DIFFRACTION99
4.8144-29.73110.19151470.19052842X-RAY DIFFRACTION98

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