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

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Basic information

Entry
Database: PDB / ID: 5mha
TitleD-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with a mixture of 2-ketohexanoic acid and 2-hydroxyhexanoic acid, and NADPH (1.57 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 / (2R)-2-hydroxyhexanoic acid / Chem-NDP / D-2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesHaloferax mediterranei ATCC 33500 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsBisson, C. / Baker, P.J. / Domenech Perez, J. / Pramanpol, N. / Harding, S.E. / Rice, D.W. / Ferrer, J.
Funding support Spain, United Kingdom, 4items
OrganizationGrant numberCountry
University of AlicanteVIGROB046 Spain
Biotechnology and Biological Sciences Research Council United Kingdom
Wellcome Trust United Kingdom
Wolfson Foundation United Kingdom
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 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 2.0Dec 28, 2022Group: Atomic model / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 3.0Jun 19, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / entity_src_gen / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _entity_src_gen.pdbx_gene_src_scientific_name

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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)69,38223
Polymers66,7362
Non-polymers2,64621
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-72 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.540, 76.300, 66.990
Angle α, β, γ (deg.)90.00, 97.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein D-2-hydroxyacid dehydrogenase / D2-HDH / D-specific 2-hydroxyacid dehydrogenase


Mass: 33367.992 Da / Num. of mol.: 2
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, 467 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-7N5 / 2-Ketohexanoic acid


Mass: 130.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O3
#5: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-7N6 / (2R)-2-hydroxyhexanoic acid


Mass: 132.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.38 Å3/Da / Density % sol: 48.25 %
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: 0.1 M Tris-HCl pH8, 0.5 M Mg acetate and 24 % PEG3350 Ligands: 5 mM NADPH and 50 mM 2-ketohexanoic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.57→38.15 Å / Num. obs: 81835 / % possible obs: 94.8 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 13.6
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.2 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→38.15 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.991 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.092 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21602 4104 5 %RANDOM
Rwork0.17355 ---
obs0.17571 77708 94.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.656 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20 Å20.42 Å2
2--0.88 Å20 Å2
3---1.03 Å2
Refinement stepCycle: 1 / Resolution: 1.57→38.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 167 446 5311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194988
X-RAY DIFFRACTIONr_bond_other_d0.0020.024554
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9856810
X-RAY DIFFRACTIONr_angle_other_deg0.974310468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1855622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18123.782238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06415714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2281541
X-RAY DIFFRACTIONr_chiral_restr0.0830.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215676
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021109
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_it16.8292.5592473
X-RAY DIFFRACTIONr_mcbond_other16.8292.5582472
X-RAY DIFFRACTIONr_mcangle_it14.5213.7723091
X-RAY DIFFRACTIONr_mcangle_other14.5193.7733092
X-RAY DIFFRACTIONr_scbond_it33.1333.3052515
X-RAY DIFFRACTIONr_scbond_other33.1423.3012512
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other25.3984.5143711
X-RAY DIFFRACTIONr_long_range_B_refined22.84932.4955586
X-RAY DIFFRACTIONr_long_range_B_other22.84732.4925587
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.574→1.615 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 289 -
Rwork0.301 5683 -
obs--93.55 %

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