[English] 日本語
Yorodumi
- PDB-2e68: Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogena... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2.0E+68
TitleCrystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with dihydroorotate
ComponentsDihydroorotate dehydrogenase
KeywordsOXIDOREDUCTASE / Chagas disease / Pyrimidine Biosynthesis / Dihydroorotate Dehydrogenase / Fumarate Reductase / Energy Metabolism / Redox Homeostasis / Flavoprotein
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / 'de novo' UMP biosynthetic process / cytoplasm
Similarity search - Function
Dihydroorotate Dehydrogenase A; chain A, domain 2 / Dihydroorotate Dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / Roll ...Dihydroorotate Dehydrogenase A; chain A, domain 2 / Dihydroorotate Dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-DOR / FLAVIN MONONUCLEOTIDE / COBALT HEXAMMINE(III) / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsInaoka, D.K. / Shimizu, H. / Sakamoto, K. / Shiba, T. / Kurisu, G. / Nara, T. / Aoki, T. / Harada, S. / Kita, K.
CitationJournal: To be Published
Title: Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with dihydroorotate
Authors: Inaoka, D.K. / Shimizu, H. / Sakamoto, K. / Shiba, T. / Kurisu, G. / Nara, T. / Aoki, T. / Harada, S. / Kita, K.
History
DepositionDec 26, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydroorotate dehydrogenase
B: Dihydroorotate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,15511
Polymers68,3972
Non-polymers1,7589
Water11,385632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-35 kcal/mol
Surface area21190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.443, 71.944, 123.852
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Dihydroorotate dehydrogenase


Mass: 34198.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: TALAHUEN / Gene: tcdhod2 / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q4D3W2, EC: 1.3.3.1

-
Non-polymers , 5 types, 641 molecules

#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-DOR / (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID / DIHYDROOROTIC ACID


Mass: 158.112 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6N2O4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 18% PEG 3350, 1mM Oxonic acid potassium salt, 0.25M Hexammine cobalt trichloride, 0.1M cacodylate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 28, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. all: 126103 / Num. obs: 122937 / % possible obs: 97.5 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.5
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 4.26 / Num. unique all: 12338 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E6A

2e6a


Resolution: 1.38→29.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.724 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.058 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18286 6159 5 %RANDOM
Rwork0.16846 ---
obs0.16919 116503 97.23 %-
all-126157 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.754 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.38→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4763 0 115 632 5510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225093
X-RAY DIFFRACTIONr_angle_refined_deg1.1982.0116943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5135662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42924.01207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.92615829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.261528
X-RAY DIFFRACTIONr_chiral_restr0.080.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023862
X-RAY DIFFRACTIONr_nbd_refined0.1970.22485
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23545
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2467
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.330.229
X-RAY DIFFRACTIONr_mcbond_it0.5591.53279
X-RAY DIFFRACTIONr_mcangle_it0.87325130
X-RAY DIFFRACTIONr_scbond_it1.48232108
X-RAY DIFFRACTIONr_scangle_it2.3564.51791
LS refinement shellResolution: 1.38→1.415 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 464 -
Rwork0.204 8409 -
obs--96.51 %

+
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