[English] 日本語
Yorodumi
- PDB-8jdd: Crystal structure of H405A mLDHD in apo form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jdd
TitleCrystal structure of H405A mLDHD in apo form
ComponentsProbable D-lactate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / D-lactate dehydrogenase / LDHD / 2-hydroxyacid
Function / homology
Function and homology information


D-lactate dehydrogenase (cytochrome) / lactate catabolic process / D-lactate dehydrogenase (cytochrome) activity / Mitochondrial protein import / D-lactate dehydrogenase (NAD+) activity / ATP biosynthetic process / Mitochondrial protein degradation / FAD binding / mitochondrial inner membrane / mitochondrion
Similarity search - Function
FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / 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
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Probable D-lactate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsJin, S. / Chen, X. / Yang, J. / Ding, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870723 China
Chinese Academy of SciencesXDB37030305 China
CitationJournal: Nat Commun / Year: 2023
Title: Lactate dehydrogenase D is a general dehydrogenase for D-2-hydroxyacids and is associated with D-lactic acidosis.
Authors: Jin, S. / Chen, X. / Yang, J. / Ding, J.
History
DepositionMay 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: 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 / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable D-lactate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1712
Polymers50,3861
Non-polymers7861
Water6,792377
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.970, 103.400, 122.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-644-

HOH

21A-924-

HOH

31A-968-

HOH

-
Components

#1: Protein Probable D-lactate dehydrogenase, mitochondrial / DLD / Lactate dehydrogenase D


Mass: 50385.789 Da / Num. of mol.: 1 / Mutation: H405A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ldhd / Production host: Escherichia coli (E. coli)
References: UniProt: Q7TNG8, D-lactate dehydrogenase (cytochrome)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 4.0 M sodium formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.55→63.75 Å / Num. obs: 73286 / % possible obs: 98.5 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Χ2: 0.91 / Net I/σ(I): 21.4 / Num. measured all: 806063
Reflection shellResolution: 1.55→1.59 Å / % possible obs: 87.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.613 / Num. measured all: 21550 / Num. unique obs: 4764 / CC1/2: 0.721 / Rpim(I) all: 0.314 / Rrim(I) all: 0.695 / Χ2: 0.57 / Net I/σ(I) obs: 2.7

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→29.75 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1869 3664 5 %
Rwork0.1704 --
obs0.1712 73278 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 53 377 3843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073554
X-RAY DIFFRACTIONf_angle_d1.0454845
X-RAY DIFFRACTIONf_dihedral_angle_d13.546492
X-RAY DIFFRACTIONf_chiral_restr0.062555
X-RAY DIFFRACTIONf_plane_restr0.007633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.25951160.24772332X-RAY DIFFRACTION86
1.57-1.590.24871350.21972384X-RAY DIFFRACTION89
1.59-1.610.24961410.21442473X-RAY DIFFRACTION92
1.61-1.640.2281470.20032546X-RAY DIFFRACTION95
1.64-1.660.21011430.19452632X-RAY DIFFRACTION97
1.66-1.690.20541150.18792719X-RAY DIFFRACTION99
1.69-1.720.21081450.17662674X-RAY DIFFRACTION100
1.72-1.750.21311370.17572699X-RAY DIFFRACTION100
1.75-1.790.21141450.17732688X-RAY DIFFRACTION100
1.79-1.820.22061410.17892703X-RAY DIFFRACTION100
1.82-1.860.20281440.19212694X-RAY DIFFRACTION100
1.86-1.910.20141350.17722715X-RAY DIFFRACTION100
1.91-1.950.20071390.18022707X-RAY DIFFRACTION100
1.95-2.010.20941430.17832689X-RAY DIFFRACTION100
2.01-2.060.17561440.17232706X-RAY DIFFRACTION100
2.06-2.130.18331460.17122727X-RAY DIFFRACTION100
2.13-2.210.17731380.16762685X-RAY DIFFRACTION100
2.21-2.30.18161610.182738X-RAY DIFFRACTION100
2.3-2.40.22071450.17252697X-RAY DIFFRACTION100
2.4-2.530.20871320.17792749X-RAY DIFFRACTION100
2.53-2.680.20461510.18372707X-RAY DIFFRACTION100
2.68-2.890.1971490.18792756X-RAY DIFFRACTION100
2.89-3.180.18881320.17912743X-RAY DIFFRACTION100
3.18-3.640.19511400.15992770X-RAY DIFFRACTION100
3.64-4.590.15591350.14222792X-RAY DIFFRACTION100
4.59-29.750.15381650.1592889X-RAY DIFFRACTION100

+
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