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- PDB-3wx0: The crystal structure of D-lactate dehydrogenase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 3wx0
TitleThe crystal structure of D-lactate dehydrogenase from Escherichia coli
ComponentsD-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
KeywordsOXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / NADH binding
Function / homology
Function and homology information


D-lactate dehydrogenase / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / cytosol
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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 ...D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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 NAD-binding / D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsFurukawa, N. / Togawa, M. / Miyanaga, A. / Nakajima, M. / Taguchi, H.
CitationJournal: To be Published
Title: Allosteric D-lactate dehydrogenases from three Gram-negative bacteria
Authors: Furukawa, N. / Togawa, M. / Miyanaga, A. / Nakajima, M. / Taguchi, H.
History
DepositionJul 8, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
B: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
C: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
D: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding


Theoretical massNumber of molelcules
Total (without water)154,3844
Polymers154,3844
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.029, 131.029, 405.746
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAGLYGLYAA4 - 32120 - 337
21ALAALACYSCYSBB4 - 32420 - 340
12ALAALAASNASNAA4 - 31420 - 330
22ALAALAASNASNCC4 - 31420 - 330
13LEULEUASNASNAA3 - 31719 - 333
23LEULEUASNASNDD3 - 31719 - 333
14ALAALAASNASNBB4 - 31420 - 330
24ALAALAASNASNCC4 - 31420 - 330
15ALAALASERSERBB4 - 31620 - 332
25ALAALASERSERDD4 - 31620 - 332
16ALAALAASNASNCC4 - 31420 - 330
26ALAALAASNASNDD4 - 31420 - 330

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding / D-lactate dehydrogenase / D-2-hydroxyacid dehydrogenase


Mass: 38595.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: B21_01364, ECBD_2243, ECD_01352, ldhA / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: C6EEW4, UniProt: A0A140N893*PLUS, D-lactate dehydrogenase

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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: 3.26 Å3/Da / Density % sol: 62.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100mM sodium acetate (pH 4.5), 0.8M sodium dihydrogenphosphate, 1.2M potassium monohydrogen phosphate., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2012
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→55.03 Å / Num. all: 32130 / Num. obs: 32128 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.3→3.48 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J49

1j49


Resolution: 3.3→55.03 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.867 / SU B: 20.876 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R Free: 0.489 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27116 1631 5.1 %RANDOM
Rwork0.23143 ---
obs0.23347 30412 99.95 %-
all-32046 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.62 Å20 Å2
2--0.62 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 3.3→55.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8746 0 0 0 8746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198926
X-RAY DIFFRACTIONr_bond_other_d0.0050.028615
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.96312041
X-RAY DIFFRACTIONr_angle_other_deg1.071319750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95551115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93924.272405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.078151543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6691550
X-RAY DIFFRACTIONr_chiral_restr0.080.21376
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210115
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022073
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_it5.1467.2324511
X-RAY DIFFRACTIONr_mcbond_other5.1437.2324510
X-RAY DIFFRACTIONr_mcangle_it8.00210.8385609
X-RAY DIFFRACTIONr_mcangle_other8.00210.8385610
X-RAY DIFFRACTIONr_scbond_it5.1447.654414
X-RAY DIFFRACTIONr_scbond_other5.1437.654415
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.27911.3436432
X-RAY DIFFRACTIONr_long_range_B_refined11.06357.3029914
X-RAY DIFFRACTIONr_long_range_B_other11.06357.3049915
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A161720.07
12B161720.07
21A161930.07
22C161930.07
31A177840.06
32D177840.06
41B144800.09
42C144800.09
51B154350.08
52D154350.08
61C155530.07
62D155530.07
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 129 -
Rwork0.306 2166 -
obs--100 %

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