[English] 日本語
Yorodumi
- PDB-1dor: DIHYDROOROTATE DEHYDROGENASE A FROM LACTOCOCCUS LACTIS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dor
TitleDIHYDROOROTATE DEHYDROGENASE A FROM LACTOCOCCUS LACTIS
ComponentsDIHYDROOROTATE DEHYDROGENASE A
KeywordsOXIDOREDUCTASE / PYRIMIDINE NUCLEOTIDE BIOSYNTHESIS
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1 / 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 signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / Dihydroorotate dehydrogenase domain ...Dihydroorotate dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1 / 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 signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / 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
FLAVIN MONONUCLEOTIDE / Dihydroorotate dehydrogenase A (fumarate) / Dihydroorotate dehydrogenase A (fumarate)
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsRowland, P. / Larsen, S.
Citation
Journal: Structure / Year: 1997
Title: The crystal structure of the flavin containing enzyme dihydroorotate dehydrogenase A from Lactococcus lactis.
Authors: Rowland, P. / Nielsen, F.S. / Jensen, K.F. / Larsen, S.
#1: Journal: Protein Sci. / Year: 1996
Title: Purification and Characterization of Dihydroorotate Dehydrogenase a from Lactococcus Lactis, Crystallization and Preliminary X-Ray Diffraction Studies of the Enzyme
Authors: Nielsen, F.S. / Rowland, P. / Larsen, S. / Jensen, K.F.
History
DepositionJan 14, 1997Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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 A
B: DIHYDROOROTATE DEHYDROGENASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3974
Polymers68,4842
Non-polymers9132
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-43 kcal/mol
Surface area22570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.190, 109.230, 67.170
Angle α, β, γ (deg.)90.00, 104.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8728, 0.0049, 0.4881), (0.0052, -1, 0.0008), (0.4881, 0.0019, -0.8728)
Vector: -8.65, 64.2123, 32.4427)

-
Components

#1: Protein DIHYDROOROTATE DEHYDROGENASE A


Mass: 34242.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lactococcus lactis (lactic acid bacteria)
References: UniProt: P54321, UniProt: A2RJT9*PLUS, EC: 1.3.3.1
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYSTEINE RESIDUES A 130 AND B 130 ARE PROBABLY OXIDIZED IN THIS CRYSTAL STRUCTURE. BOTH HAVE EXTRA ...CYSTEINE RESIDUES A 130 AND B 130 ARE PROBABLY OXIDIZED IN THIS CRYSTAL STRUCTURE. BOTH HAVE EXTRA SIDE CHAIN DENSITY BEYOND THEIR SG ATOMS, AND IN AN FO-FC DIFFERENCE MAP CALCULATED USING THE REFINED PROTEIN PHASES THE TWO LARGEST POSITIVE PEAKS CORRESPOND TO THESE POSITIONS. THESE TWO PEAKS ARE PROBABLY DUE TO A SINGLE OXYGEN ATOM COVALENTLY BONDED TO THE CYSTEINE SG ATOMS. THE COORDINATES OF THE TWO FO-FC PEAKS ARE AS FOLLOWS. A 130 PEAK (7.387,47.288,16.024) 2.4 ANGSTROMS FROM A 130 S B 130 PEAK (5.540,17.078,22.161) 2.1 ANGSTROMS FROM B 130 S ATOMS HAVE NOT BEEN INCLUDED IN THESE POSITIONS AND WERE NOT INCLUDED DURING ANY OF THE REFINEMENT STEPS. SEE MAIN JOURNAL REFERENCE FOR FURTHER DETAILS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLISED FROM A SOLUTION CONTAINING 30% PEG 6000, 0.2M SODIUM ACETATE AND 0.1M TRIS-HCL, PH 8.5.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %PEG60001reservoir
20.2 Msodium acetate1reservoir
30.1 MTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 50757 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 22.9 Å2 / Rsym value: 0.052 / Net I/σ(I): 22.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.234 / % possible all: 90.8
Reflection
*PLUS
Num. measured all: 179624 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 90.8 % / Rmerge(I) obs: 0.234

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2→25 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: R-FREE
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2060 4 %THIN SHELLS
Rwork0.168 ---
obs0.168 50732 99.3 %-
Displacement parametersBiso mean: 26.7 Å2
Refine analyzeLuzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 62 353 5233
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.591
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.44
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.685
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it2.6
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2→2.03 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 103 4 %
Rwork0.253 2234 -
obs--90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM11.DNATOPH11.DNA
X-RAY DIFFRACTION4PARAM.FMNTOPOLOGY.FMN
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Num. reflection all: 50732 / Num. reflection obs: 48672
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.44
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.685

+
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