[English] 日本語
Yorodumi
- PDB-8qza: D-2-hydroxyacid dehydrogenase (D2-HDH) from Haloferax mediterrane... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qza
TitleD-2-hydroxyacid dehydrogenase (D2-HDH) from Haloferax mediterranei apo-enzyme (2.25 A resolution)
ComponentsD-2-hydroxyacid dehydrogenase
KeywordsOXIDOREDUCTASE / halophilic adaptation domain closure mechanism
Function / homology
Function and homology information


NADH binding / carboxylic acid binding / carboxylic acid metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NADPH binding
Similarity search - Function
: / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
D-2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesHaloferax mediterranei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.252 Å
AuthorsBaker, P.J. / Barrett, J.R. / Dakhil, A.A.A.B. / Domenech, J. / Bisson, C. / Pramanpol, N. / Sedelnikova, S.E. / Ferrer, J. / Rice, D.W.
Funding support United Kingdom, Spain, Thailand, Libya, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/1003703/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/D524975/1 United Kingdom
Other governmentGV05/166 Spain
Other government Thailand
Other governmentLibya
CitationJournal: Commun Biol / Year: 2025
Title: Potassium binding by carbonyl clusters, halophilic adaptation and catalysis of Haloferax mediterranei D-2-hydroxyacid dehydrogenase.
Authors: Domenech, J. / Pramanpol, N. / Bisson, C. / Sedelnikova, S.E. / Barrett, J.R. / Dakhil, A.A.A.B. / Mykhaylyk, V. / Abdelhameed, A.S. / Harding, S.E. / Rice, D.W. / Baker, P.J. / Ferrer, J.
History
DepositionOct 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-2-hydroxyacid dehydrogenase
B: D-2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9039
Polymers66,7362
Non-polymers1687
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, also ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-77 kcal/mol
Surface area25410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.352, 75.986, 74.589
Angle α, β, γ (deg.)90.000, 93.991, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 308 / Label seq-ID: 1 - 308

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein D-2-hydroxyacid dehydrogenase


Mass: 33367.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax mediterranei (archaea) / Gene: ddh / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2VEQ7
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.5 % / Description: blocks
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein Buffer: 20mM Tris/HCl pH 8.0 2mM EDTA 1M NaCl Crystallization condition: 0.1 M TRIS/HCl pH 8.0 0.5 M Magnesium acetate 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.25→29.45 Å / Num. obs: 32656 / % possible obs: 98.8 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rpim(I) all: 0.041 / Net I/σ(I): 11.9
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 5.1 % / Num. unique obs: 2669 / CC1/2: 0.79 / Rpim(I) all: 0.42 / % possible all: 88

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.252→29.45 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 16.083 / SU ML: 0.187 / Cross valid method: FREE R-VALUE / ESU R: 0.277 / ESU R Free: 0.227
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2512 1645 5.04 %
Rwork0.1899 30994 -
all0.193 --
obs-32639 98.774 %
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: 65.302 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å21.126 Å2
2--2.006 Å20 Å2
3----0.508 Å2
Refinement stepCycle: LAST / Resolution: 2.252→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 7 70 4775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124804
X-RAY DIFFRACTIONr_bond_other_d0.0030.0164376
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.6556560
X-RAY DIFFRACTIONr_angle_other_deg0.7441.57310066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2195614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.921540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33910708
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.23710234
X-RAY DIFFRACTIONr_chiral_restr0.0970.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025828
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021072
X-RAY DIFFRACTIONr_nbd_refined0.2110.2916
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.24100
X-RAY DIFFRACTIONr_nbtor_refined0.1640.22355
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22576
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2121
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.110.210
X-RAY DIFFRACTIONr_nbd_other0.1690.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.29
X-RAY DIFFRACTIONr_mcbond_it7.3745.2932462
X-RAY DIFFRACTIONr_mcbond_other7.3745.2922462
X-RAY DIFFRACTIONr_mcangle_it10.679.5053074
X-RAY DIFFRACTIONr_mcangle_other10.6699.5083075
X-RAY DIFFRACTIONr_scbond_it7.6455.7942342
X-RAY DIFFRACTIONr_scbond_other7.6445.7972343
X-RAY DIFFRACTIONr_scangle_it11.16110.4333486
X-RAY DIFFRACTIONr_scangle_other11.1610.4353487
X-RAY DIFFRACTIONr_lrange_it13.86952.845048
X-RAY DIFFRACTIONr_lrange_other13.88552.9095032
X-RAY DIFFRACTIONr_ncsr_local_group_10.1320.058755
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.131550.05007
12AX-RAY DIFFRACTIONLocal ncs0.131550.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.252-2.310.3311250.28219300.28524200.9190.94184.91740.264
2.31-2.3730.31410.25921960.26123390.9360.95499.91450.243
2.373-2.4410.2621150.2221630.22222780.9540.9681000.201
2.441-2.5160.2831190.22421460.22722660.9460.96899.95590.204
2.516-2.5980.27940.23720510.23921470.9510.96599.90680.213
2.598-2.6880.318910.22719970.23120900.9420.97199.90430.204
2.688-2.7890.292850.21119310.21420160.9410.9741000.183
2.789-2.9020.314940.20218310.20719270.9430.97799.89620.176
2.902-3.0290.2711060.1917850.19418910.9590.9781000.169
3.029-3.1760.247960.19616790.19917770.9490.97699.88750.175
3.176-3.3450.272760.20316240.20617020.9610.97699.88250.187
3.345-3.5450.315710.20415370.20916090.9450.9899.93790.194
3.545-3.7860.2850.18314410.18415260.9760.9861000.175
3.786-4.0840.23690.17813420.18114110.9710.9841000.173
4.084-4.4650.171530.1512780.15113310.9850.9871000.149
4.465-4.9780.229600.14311140.14711740.9670.9871000.145
4.978-5.7210.307510.17110040.17710590.9590.98299.62230.172
5.721-6.9410.245510.198530.1939050.9710.98399.88950.194
6.941-9.5540.199350.1486740.1517110.9740.98899.71870.164
9.554-29.450.228280.2144180.2154470.9660.97599.77630.238
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1708-0.1515-0.11820.03030.00060.03840.04140.20120.0835-0.0025-0.0499-0.0359-0.01110.04050.00850.0056-0.01210.0140.2045-0.0010.155321.23760.160716.2685
20.79750.16930.12730.0510.0420.0870.0268-0.0731-0.02570.0099-0.03010.0344-0.0118-0.06310.00330.043-0.01010.02190.1426-0.01660.1266-4.2414-6.218138.0431
Refinement TLS groupSelection: ALL

+
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