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

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Basic information

Entry
Database: PDB / ID: 4ylw
TitleCrystal structure of human dihydroorotate dehydrogenase (DHODH) with No.33 compound
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrialDihydroorotate dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Inhibitor / Rheumatoid Arthritis / Complex / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


dihydroorotate dehydrogenase (quinone) / pyrimidine ribonucleotide biosynthetic process / 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 ...dihydroorotate dehydrogenase (quinone) / pyrimidine ribonucleotide biosynthetic process / 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 / integral component of membrane / nucleoplasm / cytosol
Similarity search - Function
Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase, conserved site / Dihydroorotate dehydrogenase / Dihydroorotate dehydrogenase domain / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-52Y / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsWu, D. / Ouyang, P. / Lu, W. / Huang, J.
CitationJournal: To Be Published
Title: Crystal structure of human dihydroorotate dehydrogenase (DHODH) with No.33 compound
Authors: Wu, D. / Ouyang, P. / Lu, W. / Huang, J.
History
DepositionMar 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release

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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)44,60814
Polymers42,6361
Non-polymers1,97113
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-19 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.721, 90.721, 123.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-654-

HOH

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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: 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 / Plasmid: pET19B / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone)

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Non-polymers , 5 types, 167 molecules

#2: Chemical ChemComp-52Y / methyl (2Z)-cyano[3-(3-fluoro-4'-methoxybiphenyl-4-yl)-4-oxo-1,3-thiazolidin-2-ylidene]acetate


Mass: 398.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15FN2O4S
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


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


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.11 % / Description: Yellow cube like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M acetate, 40mM UDAO, 20.8mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM DHO, 1.6-1.8M ammonium sulfate
PH range: 4.8-6.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→28.64 Å / Num. obs: 53848 / % possible obs: 99.89 % / Redundancy: 10.1 % / Net I/σ(I): 11.7
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 5.7 / % possible all: 99.89

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JTS
Resolution: 1.79→28.64 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.403 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17822 1995 3.6 %RANDOM
Rwork0.15461 ---
obs0.15545 53848 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.646 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.79→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 120 154 3059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0192959
X-RAY DIFFRACTIONr_bond_other_d0.0010.022864
X-RAY DIFFRACTIONr_angle_refined_deg2.4662.0274017
X-RAY DIFFRACTIONr_angle_other_deg0.99136566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4915369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58622.937126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86615497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6421531
X-RAY DIFFRACTIONr_chiral_restr0.1410.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213322
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02657
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3621.8711461
X-RAY DIFFRACTIONr_mcbond_other2.361.8681460
X-RAY DIFFRACTIONr_mcangle_it3.3322.791826
X-RAY DIFFRACTIONr_mcangle_other3.3312.7931827
X-RAY DIFFRACTIONr_scbond_it4.9152.5381497
X-RAY DIFFRACTIONr_scbond_other4.9132.541498
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7863.6062189
X-RAY DIFFRACTIONr_long_range_B_refined8.64416.3293438
X-RAY DIFFRACTIONr_long_range_B_other8.64616.3373439
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.788→1.834 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 146 -
Rwork0.174 3897 -
obs--99.21 %

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