[English] 日本語
Yorodumi
- PDB-6lpt: Crystal structure of human D-2-hydroxyglutarate dehydrogenase in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lpt
TitleCrystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-lactate (D-LAC)
ComponentsD-2-hydroxyglutarate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / dehydrogenase / FLAVOPROTEIN
Function / homology
Function and homology information


D-2-hydroxyglutarate dehydrogenase / (R)-2-hydroxyglutarate dehydrogenase activity / tartrate metabolic process / Interconversion of 2-oxoglutarate and 2-hydroxyglutarate / malate metabolic process / response to cobalt ion / 2-oxoglutarate metabolic process / response to manganese ion / lactate metabolic process / response to zinc ion ...D-2-hydroxyglutarate dehydrogenase / (R)-2-hydroxyglutarate dehydrogenase activity / tartrate metabolic process / Interconversion of 2-oxoglutarate and 2-hydroxyglutarate / malate metabolic process / response to cobalt ion / 2-oxoglutarate metabolic process / response to manganese ion / lactate metabolic process / response to zinc ion / FAD binding / mitochondrial matrix / mitochondrion / zinc ion binding
Similarity search - Function
Alpha-Beta Plaits - #2190 / Alpha-Beta Plaits - #2740 / : / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 ...Alpha-Beta Plaits - #2190 / Alpha-Beta Plaits - #2740 / : / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / LACTIC ACID / D-2-hydroxyglutarate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.621 Å
AuthorsYang, J. / Zhu, H. / Ding, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870723 China
National Natural Science Foundation of China (NSFC)31530013 China
CitationJournal: Cell Discov / Year: 2021
Title: Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations.
Authors: Yang, J. / Zhu, H. / Zhang, T. / Ding, J.
History
DepositionJan 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-2-hydroxyglutarate dehydrogenase, mitochondrial
B: D-2-hydroxyglutarate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5488
Polymers104,6662
Non-polymers1,8826
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8850 Å2
ΔGint-127 kcal/mol
Surface area32460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.263, 94.411, 73.575
Angle α, β, γ (deg.)90.000, 111.770, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein D-2-hydroxyglutarate dehydrogenase, mitochondrial


Mass: 52332.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: D2HGDH, D2HGD / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N465, Oxidoreductases; Acting on the CH-OH group of donors; With unknown physiological acceptors
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-LAC / LACTIC ACID


Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M BIS-TRIS, pH 6.5, 25% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9788 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.62→50 Å / Num. obs: 27511 / % possible obs: 99.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.063 / Rrim(I) all: 0.166 / Χ2: 0.467 / Net I/σ(I): 3 / Num. measured all: 188447
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.62-2.7170.65627380.8410.2650.7080.41499.9
2.71-2.826.90.55927650.8680.2270.6040.41899.9
2.82-2.956.90.41827320.9280.170.4520.42799.9
2.95-3.116.90.34127310.9420.1390.3690.44299.6
3.11-3.36.20.24127270.9670.1040.2630.45298.8
3.3-3.567.20.17527600.9870.070.1890.47399.9
3.56-3.917.10.1327370.9920.0520.140.599.5
3.91-4.486.90.08527750.9950.0350.0920.5299.6
4.48-5.646.70.07327450.9960.030.0790.5198.8
5.64-506.70.0628010.9980.0250.0650.5199.1

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LPN

6lpn


Resolution: 2.621→36.387 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 1297 4.73 %
Rwork0.1912 26135 -
obs0.1931 27432 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.23 Å2 / Biso mean: 34.5101 Å2 / Biso min: 9.13 Å2
Refinement stepCycle: final / Resolution: 2.621→36.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7027 0 120 206 7353
Biso mean--28.28 31.17 -
Num. residues----933
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.621-2.72560.31281480.2409285998
2.7256-2.84960.26191550.21582898100
2.8496-2.99980.26351540.20822889100
2.9998-3.18760.25031220.21152925100
3.1876-3.43360.2581620.193288299
3.4336-3.77880.23371210.1752937100
3.7788-4.32480.18971210.16072948100
4.3248-5.44590.19591570.1677289699
5.4459-36.3870.22311570.2144290197

+
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