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- PDB-8ofw: Crystal structure of the full-length dihydroorotate dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 8ofw
TitleCrystal structure of the full-length dihydroorotate dehydrogenase from Mycobacterium tuberculosis
ComponentsDihydroorotate dehydrogenase (quinone)Dihydroorotate dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE / dihydroorotate dehydrogenase / Flavoenzyme / Pyrimidine biosynthesis
Function / homology
Function and homology information


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / plasma membrane / cytoplasm
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-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Dihydroorotate dehydrogenase (quinone)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsAlberti, M. / Ferraris, D.M. / Miggiano, R.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca Italy
CitationJournal: Febs Lett. / Year: 2023
Title: Biochemical characterization of Mycobacterium tuberculosis dihydroorotate dehydrogenase and identification of a selective inhibitor.
Authors: Alberti, M. / Sainas, S. / Ronchi, E. / Lolli, M.L. / Boschi, D. / Rizzi, M. / Ferraris, D.M. / Miggiano, R.
History
DepositionMar 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,3534
Polymers80,4402
Non-polymers9132
Water0
1
A: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6762
Polymers40,2201
Non-polymers4561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6762
Polymers40,2201
Non-polymers4561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.050, 85.215, 181.005
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS oper: (Code: givenMatrix: (-0.999321541726, -0.0309324818799, 0.0199909431206), (0.0284020368173, -0.992796540085, -0.116397398167), (0.0234473995728, -0.115750643887, 0.993001514547)Vector: -23. ...NCS oper: (Code: given
Matrix: (-0.999321541726, -0.0309324818799, 0.0199909431206), (0.0284020368173, -0.992796540085, -0.116397398167), (0.0234473995728, -0.115750643887, 0.993001514547)
Vector: -23.7445162631, -42.6435875142, 3.60776600075)

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Components

#1: Protein Dihydroorotate dehydrogenase (quinone) / Dihydroorotate dehydrogenase (quinone) / DHOdehase / DHOD / DHODase / Dihydroorotate oxidase


Mass: 40219.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pyrD, Rv2139, MTCY270.29c / Production host: Escherichia coli (E. coli)
References: UniProt: P9WHL1, dihydroorotate dehydrogenase (quinone)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0,2 M Sodium Chloride, 0,1 M Tris-HCl pH 8,5 and 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 3.8→41.508 Å / Num. obs: 39498 / % possible obs: 97.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 116.1 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.253 / Rrim(I) all: 0.279 / Net I/σ(I): 5
Reflection shellResolution: 3.8→4 Å / Rmerge(I) obs: 1.229 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1012 / CC1/2: 0.688 / Rrim(I) all: 1.358

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→41.508 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.856 / WRfactor Rfree: 0.307 / WRfactor Rwork: 0.235 / SU B: 92.873 / SU ML: 1.209 / Average fsc free: 0.9077 / Average fsc work: 0.9303 / Cross valid method: FREE R-VALUE / ESU R Free: 1.126
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3278 354 4.921 %
Rwork0.2551 6840 -
all0.259 --
obs-7194 95.869 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 125.462 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20 Å2
2--16.102 Å2-0 Å2
3----14.653 Å2
Refinement stepCycle: LAST / Resolution: 3.8→41.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5192 0 62 0 5254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125361
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165258
X-RAY DIFFRACTIONr_angle_refined_deg0.9741.6487305
X-RAY DIFFRACTIONr_angle_other_deg0.3431.56912019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3565687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.976568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63710821
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.23810216
X-RAY DIFFRACTIONr_chiral_restr0.0490.2840
X-RAY DIFFRACTIONr_chiral_restr_other0.0130.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026476
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021252
X-RAY DIFFRACTIONr_nbd_refined0.1950.21397
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.25624
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22758
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22954
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2162
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0730.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2440.254
X-RAY DIFFRACTIONr_nbd_other0.260.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2710.28
X-RAY DIFFRACTIONr_mcbond_it9.8312.1692763
X-RAY DIFFRACTIONr_mcbond_other9.8312.172763
X-RAY DIFFRACTIONr_mcangle_it16.31521.8753445
X-RAY DIFFRACTIONr_mcangle_other16.31421.8743446
X-RAY DIFFRACTIONr_scbond_it9.23213.0842598
X-RAY DIFFRACTIONr_scbond_other9.2313.0882595
X-RAY DIFFRACTIONr_scangle_it15.70723.6643860
X-RAY DIFFRACTIONr_scangle_other15.70523.6623861
X-RAY DIFFRACTIONr_lrange_it27.768153.50922225
X-RAY DIFFRACTIONr_lrange_other27.768153.50622226
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.8-3.8980.466290.394760.3945360.8060.81594.21640.37
3.898-4.0040.466230.3414780.3485120.8780.88697.85160.325
4.004-4.1190.393300.344660.3445080.8670.88497.63780.317
4.119-4.2440.405200.2964780.35110.8960.91897.4560.275
4.244-4.3820.326250.3014230.3034620.940.91996.96970.277
4.382-4.5340.236170.2774330.2764710.9380.91895.54140.248
4.534-4.7030.409250.2324060.2414460.8860.9596.63680.207
4.703-4.8920.347190.2194030.2254390.8790.96296.12760.199
4.892-5.1070.238190.2374070.2374350.9550.9597.9310.213
5.107-5.3520.311220.2193640.2233970.9250.96297.22920.197
5.352-5.6360.292220.2623530.2643860.9520.95697.15030.245
5.636-5.9710.339150.2433350.2473620.9160.95296.68510.224
5.971-6.3740.362220.2753070.2813400.9210.94596.76470.244
6.374-6.8710.424160.2282980.2393290.9240.96495.44070.211
6.871-7.5060.302110.2242860.2283080.9070.96496.42860.208
7.506-8.3580.283110.2272420.232730.9410.96492.6740.224
8.358-9.5870.17270.1712350.1712610.980.9892.72030.184
9.587-11.5880.113110.181940.1772180.9940.98294.03670.2
11.588-15.7840.26560.2181590.2191810.9630.96991.16020.241
15.784-41.5080.70340.397970.4051220.8520.89382.78690.415

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