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- PDB-5mh6: D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterran... -

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Basic information

Entry
Database: PDB / ID: 5mh6
TitleD-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with 2-ketohexanoic acid and NAD+ (1.35 A resolution)
ComponentsD-2-hydroxyacid dehydrogenase
KeywordsOXIDOREDUCTASE / D-2-hydroxyacid dehydrogenase / halophile / chiral specificity / reaction 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-Ketohexanoic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / D-2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesHaloferax mediterranei ATCC 33500 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBisson, C. / Baker, P.J. / Domenech Perez, J. / Pramanpol, N. / Harding, S.E. / Rice, D.W. / Ferrer, J.
Funding support United Kingdom, Spain, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
Wellcome Trust United Kingdom
Wolfson Foundation United Kingdom
University of AlicanteVIGROB046 Spain
CitationJournal: To Be Published
Title: Productive ternary complexes of D-2-hydroxyacid dehydrogenase provide insights into the chiral specificity of its reaction mechanism
Authors: Domenech Perez, J. / Pramanpol, N. / Baker, P.J. / Bisson, C. / Harding, S.E. / Rice, D.W. / Ferrer, J.
History
DepositionNov 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 2.0Jun 19, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)139,02564
Polymers133,4724
Non-polymers5,55360
Water31,3101738
1
A: D-2-hydroxyacid dehydrogenase
B: D-2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,57633
Polymers66,7362
Non-polymers2,84031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: D-2-hydroxyacid dehydrogenase
D: D-2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,44931
Polymers66,7362
Non-polymers2,71329
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.455, 75.008, 77.555
Angle α, β, γ (deg.)109.11, 107.55, 95.91
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 / D2-HDH / D-specific 2-hydroxyacid dehydrogenase


Mass: 33367.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax mediterranei ATCC 33500 (archaea)
Gene: ddh, serA5, HFX_2024 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2VEQ7, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 7 types, 1798 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Chemical
ChemComp-7N5 / 2-Ketohexanoic acid


Mass: 130.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10O3
#7: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1738 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein buffer: 20 mM Tris-HCl pH8, 3 mM EDTA and 1 M NaCl Crystallisation conditions: 0.1M Tris-HCl pH8, 0.5 M magnesium acetate and 20 % PEG3350 Ligands: 5 mM NAD+ and 50 mM 2-ketohexanoic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97204 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97204 Å / Relative weight: 1
ReflectionResolution: 1.35→46.54 Å / Num. obs: 268611 / % possible obs: 93 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.6
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.1 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→46.54 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.502 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.055 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16174 11807 5.1 %RANDOM
Rwork0.1264 ---
obs0.12817 219914 80.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.066 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0.1 Å2-0.1 Å2
2--0.18 Å20.07 Å2
3----0.21 Å2
Refinement stepCycle: 1 / Resolution: 1.35→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9360 0 346 1738 11444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910044
X-RAY DIFFRACTIONr_bond_other_d0.0020.029212
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.98313729
X-RAY DIFFRACTIONr_angle_other_deg1.423321184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8951275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.95223.693482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.546151452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3151587
X-RAY DIFFRACTIONr_chiral_restr0.0830.21550
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111468
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022255
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8241.1974963
X-RAY DIFFRACTIONr_mcbond_other2.8251.1974962
X-RAY DIFFRACTIONr_mcangle_it3.0641.7946211
X-RAY DIFFRACTIONr_mcangle_other3.0651.7946212
X-RAY DIFFRACTIONr_scbond_it6.9461.6585081
X-RAY DIFFRACTIONr_scbond_other6.9551.6585065
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7922.2777470
X-RAY DIFFRACTIONr_long_range_B_refined5.65513.08613282
X-RAY DIFFRACTIONr_long_range_B_other5.16111.57112001
X-RAY DIFFRACTIONr_rigid_bond_restr14.562319256
X-RAY DIFFRACTIONr_sphericity_free27.8875408
X-RAY DIFFRACTIONr_sphericity_bonded21.444520428
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 441 -
Rwork0.221 8606 -
obs--42.16 %

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