[English] 日本語
Yorodumi
- PDB-8ofw: Crystal structure of the full-length dihydroorotate dehydrogenase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / 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 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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)

-
Components

#1: Protein 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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more