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- PDB-2prm: The structures of apo- and inhibitor bound human dihydroorotate d... -

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Basic information

Entry
Database: PDB / ID: 2prm
TitleThe structures of apo- and inhibitor bound human dihydroorotate dehydrogenase reveal conformational flexibility within the inhibitor binding site
ComponentsDihydroorotate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / protein 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 1. / Dihydroorotate dehydrogenase signature 2. / 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
FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWalse, B. / Dufe, V.T. / Al-Karadaghi, S.
CitationJournal: Biochemistry / Year: 2008
Title: The structures of human dihydroorotate dehydrogenase with and without inhibitor reveal conformational flexibility in the inhibitor and substrate binding sites
Authors: Walse, B. / Dufe, V.T. / Svensson, B. / Fritzson, I. / Dahlberg, L. / Khairoullina, A. / Wellmar, U. / Al-Karadaghi, S.
History
DepositionMay 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4693
Polymers39,8571
Non-polymers6122
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.050, 90.050, 123.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Detailsbiological unit is a monomer

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Components

#1: Protein Dihydroorotate dehydrogenase, mitochondrial / / E.C.1.3.3.1 / Dihydroorotate oxidase / DHOdehase


Mass: 39856.535 Da / Num. of mol.: 1 / Mutation: N-terminus truncated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: mitochondriaMitochondrion / Gene: DHODH / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02127, EC: 1.3.99.11
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.62 Å3/Da / Density % sol: 65.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: DROPS WERE FORMED BY MIXING EQUAL AMOUNTS OF 18-24 MG/ML PROTEIN IN 100 MM HEPES PH 7.0, 400 MM NACL, 30% GLYCEROL, 1 MM EDTA AND 10 MM N,N- DIMETHYLUNDECYLAMIN-N-OXIDE (C11DAO) WITH A ...Details: DROPS WERE FORMED BY MIXING EQUAL AMOUNTS OF 18-24 MG/ML PROTEIN IN 100 MM HEPES PH 7.0, 400 MM NACL, 30% GLYCEROL, 1 MM EDTA AND 10 MM N,N- DIMETHYLUNDECYLAMIN-N-OXIDE (C11DAO) WITH A PRECIPITANT SOLUTION OF 0.1 M ACETATE PH 4.8 40 MM C11DAO, 20.8 MM N, N-DIMETHYLDECYLAMINE-N-OXIDE (DDAO), 2 MM DIHYDROOROTATE (DHO) THE HANGING DROPS WERE INCUBATED AGAINST 0.5 ML RESERVOIR OF 0.1 M ACETATE PH 4.8, 1.6-2.2 M AMMONIUM SULFATE AND 30% GLYCEROL., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.092 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 27, 2004 / Details: mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(III)SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.092 Å / Relative weight: 1
ReflectionResolution: 3→19.5 Å / Num. obs: 11941 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.753 Å2 / Rmerge(I) obs: 0.25 / Net I/σ(I): 6.85
Reflection shellResolution: 3→4 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 5 / Num. unique all: 6817 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D3G

1d3g


Resolution: 3→19.5 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.827 / SU B: 14.011 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.253 597 5 %RANDOM
Rwork0.19 ---
obs0.193 11938 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.718 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.34 Å20 Å2
2--0.69 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 3→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 42 31 2878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222895
X-RAY DIFFRACTIONr_angle_refined_deg1.7872.0023918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7485366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96922.88125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.45915498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7591531
X-RAY DIFFRACTIONr_chiral_restr0.1130.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022186
X-RAY DIFFRACTIONr_nbd_refined0.2420.21511
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21992
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.29
X-RAY DIFFRACTIONr_mcbond_it0.791.51854
X-RAY DIFFRACTIONr_mcangle_it1.36722904
X-RAY DIFFRACTIONr_scbond_it2.06531171
X-RAY DIFFRACTIONr_scangle_it3.5334.51014
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 42 -
Rwork0.228 800 -
obs-842 100 %

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