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- PDB-8qza: D-2-hydroxyacid dehydrogenase (D2-HDH) from Haloferax mediterrane... -

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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: To Be Published
Title: D-2-hydroxyacid dehydrogenase (D2-HDH) from Haloferax mediterranei in complex with 2-keto-hexanoic acid and NAD+ (1.16 A resolution)
Authors: Domenech, J. / Pramanpol, N. / Bisson, C. / Sedelnikova, S.E. / Barrett, J.R. / Dakhil, A.A.A.B. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)

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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

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Experimental details

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Experiment

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

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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

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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

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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

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