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- PDB-2yq4: Crystal Structure of D-isomer specific 2-hydroxyacid dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 2yq4
TitleCrystal Structure of D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii ssp. bulgaricus
ComponentsD-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / 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 ...D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / 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
D-isomer specific 2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesLACTOBACILLUS DELBRUECKII SUBSP. BULGARICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.45 Å
AuthorsHolton, S.J. / Anandhakrishnan, M. / Geerlof, A. / Wilmanns, M.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Structural Characterization of D-Isomer Specific 2-Hydroxyacid Dehydrogenase from Lactobacillus Delbrueckii Ssp. Bulgaricus
Authors: Holton, S.J. / Anandhakrishnan, M. / Geerlof, A. / Wilmanns, M.
History
DepositionNov 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE
B: D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE
C: D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE
D: D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)152,1174
Polymers152,1174
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13950 Å2
ΔGint-80.4 kcal/mol
Surface area51190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.211, 108.367, 147.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE / 2-HYDROXYACID DEHYDROGENASE


Mass: 38029.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOBACILLUS DELBRUECKII SUBSP. BULGARICUS (bacteria)
Plasmid: PETM-13 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q1GAA2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.14 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growDetails: 25% PEG 3350, 200MM MGCL2, 100MM HEPES PH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 3.45→46.72 Å / Num. obs: 19722 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 56.72 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.45→43.997 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 22.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 924 5 %
Rwork0.1793 --
obs0.1828 18458 92.2 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 7.01 Å2 / ksol: 0.295 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.9775 Å20 Å20 Å2
2--17.8825 Å20 Å2
3----7.905 Å2
Refinement stepCycle: LAST / Resolution: 3.45→43.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10154 0 0 34 10188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0210698
X-RAY DIFFRACTIONf_angle_d1.83614077
X-RAY DIFFRACTIONf_dihedral_angle_d17.2663775
X-RAY DIFFRACTIONf_chiral_restr0.1161648
X-RAY DIFFRACTIONf_plane_restr0.011784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.63190.26761110.24192283X-RAY DIFFRACTION85
3.6319-3.85930.30261220.21582431X-RAY DIFFRACTION90
3.8593-4.1570.23721520.18592438X-RAY DIFFRACTION93
4.157-4.5750.23591360.16442559X-RAY DIFFRACTION95
4.575-5.23610.2671310.16412578X-RAY DIFFRACTION95
5.2361-6.59330.28941440.18892584X-RAY DIFFRACTION95
6.5933-44.00080.18921280.14552661X-RAY DIFFRACTION92

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