[English] 日本語
Yorodumi
- PDB-7myd: Leishmania major dihydroorotate dehydrogenase in complex with 5-a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7myd
TitleLeishmania major dihydroorotate dehydrogenase in complex with 5-amino-2-(1H-pyrrol-1-yl)benzonitrile
ComponentsDihydroorotate dehydrogenase (fumarate)Dihydroorotate dehydrogenase (fumarate)
KeywordsOXIDOREDUCTASE / Leishmania major / neglected tropical disease / dihydroorotate dehydrogenase
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / fumarate metabolic process / dihydroorotate dehydrogenase activity / ciliary plasm / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleotide binding / nucleoplasm / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 5-azanyl-2-pyrrol-1-yl-benzenecarbonitrile / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPinheiro, M.P. / Cardoso, I.A. / Hunter, W.N. / Nonato, M.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2007/08703-0 Brazil
CitationJournal: To Be Published
Title: Leishmania major dihydroorotate dehydrogenase in complex with 5-amino-2-(1H-pyrrol-1-yl)benzonitrile
Authors: Pinheiro, M.P. / Cardoso, I.A. / Hunter, W.N. / Nonato, M.C.
History
DepositionMay 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Dihydroorotate dehydrogenase (fumarate)
BBB: Dihydroorotate dehydrogenase (fumarate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,15211
Polymers76,4912
Non-polymers1,6609
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-72 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.071, 143.071, 68.997
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

-
Protein , 1 types, 2 molecules AAABBB

#1: Protein Dihydroorotate dehydrogenase (fumarate) / Dihydroorotate dehydrogenase (fumarate) / Dihydroorotate oxidase


Mass: 38245.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: DHODH, LMJF_16_0530 / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q4QEW7, dihydroorotate dehydrogenase (fumarate)

-
Non-polymers , 5 types, 343 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SNQ / 5-azanyl-2-pyrrol-1-yl-benzenecarbonitrile


Mass: 183.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9N3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium citrate tribasic dihydrate, pH 5.6, 1.3 M lithium sulfate, 0.30 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.437 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.437 Å / Relative weight: 1
ReflectionResolution: 2.15→35.77 Å / Num. obs: 43015 / % possible obs: 97.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 11.9
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6253 / Rsym value: 0.803 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GYE

3gye


Resolution: 2.15→35.77 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.971 / SU ML: 0.124 / Cross valid method: FREE R-VALUE / ESU R: 0.197 / ESU R Free: 0.171
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2187 2164 5.031 %
Rwork0.1781 40847 -
all0.18 --
obs-43011 97.852 %
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: 26.369 Å2
Baniso -1Baniso -2Baniso -3
1--0.055 Å2-0.028 Å2-0 Å2
2---0.055 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.15→35.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4612 0 109 334 5055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134905
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174595
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.6416660
X-RAY DIFFRACTIONr_angle_other_deg1.2731.5710564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3945624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.42322.603219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04215777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.641524
X-RAY DIFFRACTIONr_chiral_restr0.0610.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025636
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021132
X-RAY DIFFRACTIONr_nbd_refined0.1990.21100
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.24825
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22441
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.22293
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2387
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0870.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.214
X-RAY DIFFRACTIONr_nbd_other0.1530.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.214
X-RAY DIFFRACTIONr_mcbond_it1.4212.7292484
X-RAY DIFFRACTIONr_mcbond_other1.4152.7292483
X-RAY DIFFRACTIONr_mcangle_it2.2174.0883112
X-RAY DIFFRACTIONr_mcangle_other2.2184.0883113
X-RAY DIFFRACTIONr_scbond_it1.7242.8972421
X-RAY DIFFRACTIONr_scbond_other1.7232.8982422
X-RAY DIFFRACTIONr_scangle_it2.7634.2733548
X-RAY DIFFRACTIONr_scangle_other2.7624.2743549
X-RAY DIFFRACTIONr_lrange_it3.96432.6395743
X-RAY DIFFRACTIONr_lrange_other3.92832.5865721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.2060.311970.2562974X-RAY DIFFRACTION98.3866
2.206-2.2660.3071620.2662920X-RAY DIFFRACTION97.8723
2.266-2.3320.2291470.2172851X-RAY DIFFRACTION97.846
2.332-2.4040.2771070.2112826X-RAY DIFFRACTION98.7875
2.404-2.4830.2571480.2022694X-RAY DIFFRACTION97.9662
2.483-2.570.241430.1852574X-RAY DIFFRACTION97.5583
2.57-2.6670.2191380.1712471X-RAY DIFFRACTION97.3144
2.667-2.7750.1991420.1662382X-RAY DIFFRACTION97.3015
2.775-2.8990.2341230.1782315X-RAY DIFFRACTION97.559
2.899-3.040.2151090.1722213X-RAY DIFFRACTION97.0736
3.04-3.2040.221110.1772092X-RAY DIFFRACTION97.2198
3.204-3.3990.2131160.1741996X-RAY DIFFRACTION97.8231
3.399-3.6330.182900.1711889X-RAY DIFFRACTION97.4877
3.633-3.9240.192860.161758X-RAY DIFFRACTION98.874
3.924-4.2980.178840.1311653X-RAY DIFFRACTION98.6932
4.298-4.8050.159770.1331477X-RAY DIFFRACTION99.044
4.805-5.5470.203670.1631304X-RAY DIFFRACTION98.3501
5.547-6.790.238480.1831122X-RAY DIFFRACTION97.7444
6.79-9.5880.214460.169857X-RAY DIFFRACTION97.5162
9.588-35.770.248230.221480X-RAY DIFFRACTION94.3715

+
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