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- PDB-9ibe: D-2-hydroxyacid dehydrogenase (D2HDH) from Haloferax mediterranei... -

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Basic information

Entry
Database: PDB / ID: 9ibe
TitleD-2-hydroxyacid dehydrogenase (D2HDH) from Haloferax mediterranei in complex with potassium, 2-ketohexanoic acid, NADP+ and chloride
ComponentsD-2-hydroxyacid dehydrogenase
KeywordsOXIDOREDUCTASE / Halophile / halophilic adaptation / potassium binding / complex / substrate specificity
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
2-Ketohexanoic acid / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / D-2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesHaloferax mediterranei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsBaker, P.J. / Barrett, J.R. / Dakhil, A.A.A.B. / Domenech, J. / Bisson, C. / Pramanpol, N. / Ferrer, J. / Rice, D.W.
Funding support United Kingdom, Spain, 3items
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
Generalitat ValencianaGV05/166 Spain
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
DepositionFeb 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 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
C: D-2-hydroxyacid dehydrogenase
D: D-2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,33452
Polymers133,4724
Non-polymers4,86248
Water28,2661569
1
A: D-2-hydroxyacid dehydrogenase
B: D-2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,20427
Polymers66,7362
Non-polymers2,46825
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-98 kcal/mol
Surface area23860 Å2
2
C: D-2-hydroxyacid dehydrogenase
D: D-2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,13025
Polymers66,7362
Non-polymers2,39423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10670 Å2
ΔGint-90 kcal/mol
Surface area23770 Å2
Unit cell
Length a, b, c (Å)66.633, 75.34, 78.234
Angle α, β, γ (deg.)108.841, 108.084, 95.526
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
D-2-hydroxyacid dehydrogenase


Mass: 33367.992 Da / Num. of mol.: 4
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

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Non-polymers , 6 types, 1617 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-7N5 / 2-Ketohexanoic acid


Mass: 130.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1569 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.59 Å3/Da / Density % sol: 52.5 % / Description: blocks
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: protein buffer: 20 mM Tris/HCl pH 8.0 2 mM EDTA 1 M KCl 50 mM 2-ketohexanoic acid 5 mM NAD+ Well Solution: 0.1 M Mg acetate 26 % PEG 3350 0.1 M Tris/HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.940535 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.940535 Å / Relative weight: 1
ReflectionResolution: 1.26→52.3 Å / Num. obs: 332819 / % possible obs: 92.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 11.7 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.059 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
1.26-1.283.80.8161110.330.9989.4
3.42-52.2769.9173900.990.019

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→52.276 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.204 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.047
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1876 16700 5.018 %Random
Rwork0.1518 316107 --
all0.154 ---
obs-332807 92.234 %-
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: 18.037 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0.178 Å2-0.216 Å2
2--0.191 Å20.214 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.26→52.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9396 0 268 1569 11233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01210008
X-RAY DIFFRACTIONr_bond_other_d0.0030.0169056
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.8213716
X-RAY DIFFRACTIONr_angle_other_deg0.7841.74520836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68151256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.176599
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg3.43458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.379101454
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.32610485
X-RAY DIFFRACTIONr_chiral_restr0.0990.21551
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212079
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022249
X-RAY DIFFRACTIONr_nbd_refined0.2480.21946
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.28548
X-RAY DIFFRACTIONr_nbtor_refined0.1680.24976
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.25014
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.21125
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.050.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.265
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2680.226
X-RAY DIFFRACTIONr_nbd_other0.1860.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.265
X-RAY DIFFRACTIONr_mcbond_it7.8141.5524970
X-RAY DIFFRACTIONr_mcbond_other7.8111.5524970
X-RAY DIFFRACTIONr_mcangle_it10.0122.7986220
X-RAY DIFFRACTIONr_mcangle_other10.0132.7986221
X-RAY DIFFRACTIONr_scbond_it11.6461.8765038
X-RAY DIFFRACTIONr_scbond_other11.6461.8765037
X-RAY DIFFRACTIONr_scangle_it15.123.2837488
X-RAY DIFFRACTIONr_scangle_other15.1193.2837489
X-RAY DIFFRACTIONr_lrange_it17.69220.61611640
X-RAY DIFFRACTIONr_lrange_other16.81618.44511129
X-RAY DIFFRACTIONr_rigid_bond_restr4.08319064
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
1.26-1.2930.36912150.347227270.348266300.90.91589.90610.344
1.293-1.3280.33411860.318224140.319260660.9170.92890.53940.313
1.328-1.3670.3111340.292212750.293252460.9280.93788.76260.286
1.367-1.4090.2749960.261191630.262245370.9420.94982.15760.25
1.409-1.4550.26411170.232211890.233238420.9530.9693.55760.221
1.455-1.5060.23210830.207205970.208230910.9610.96993.88940.193
1.506-1.5630.21410540.181198220.183222170.9680.97893.96410.164
1.563-1.6270.21510000.162191180.165214080.9720.98393.97420.143
1.627-1.6990.2069540.144182380.147205020.9750.98893.61040.123
1.699-1.7820.1858810.131172900.133195980.9790.9992.71860.109
1.782-1.8780.1768600.118157940.121186230.9810.99289.42710.097
1.878-1.9920.1628080.111151080.113176750.9840.99390.04810.093
1.992-2.1290.1537420.109152130.111165090.9850.99396.64420.094
2.129-2.2990.1448230.102141790.105155030.9880.99496.76840.089
2.299-2.5180.1427090.102130020.104141750.9880.99496.72660.09
2.518-2.8150.1586220.113116970.115128140.9850.99296.1370.101
2.815-3.2480.1735350.133101470.135113310.9830.9994.27240.126
3.248-3.9750.1554090.13682690.13795610.9880.99190.76460.135
3.975-5.6050.1383690.1270000.12174120.9910.99399.41990.122
5.605-52.2760.1782030.15938670.1640860.9720.98699.60840.162

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