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- PDB-4xkj: a Novel D-lactate Dehydrogenase from Sporolactobacillus sp -

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Basic information

Entry
Database: PDB / ID: 4xkj
Titlea Novel D-lactate Dehydrogenase from Sporolactobacillus sp
ComponentsD-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / D-lactate Dehydrogenase / Complex / Sporolactobacillus sp
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / D-lactate dehydrogenase
Similarity search - Component
Biological speciesSporolactobacillus inulinus CASD (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3.148 Å
AuthorsBo, Y. / Hui, D. / Xiang, L.
CitationJournal: To Be Published
Title: a Novel D-lactate Dehydrogenase from Sporolactobacillus sp
Authors: Bo, Y. / Hui, D. / Xiang, L.
History
DepositionJan 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-lactate dehydrogenase
B: D-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9134
Polymers73,5862
Non-polymers1,3272
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-35 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.263, 109.505, 113.003
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-lactate dehydrogenase


Mass: 36792.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporolactobacillus inulinus CASD (bacteria)
Strain: CASD / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3KL04*PLUS
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Ammonium acetate,Sodium citrate tribasic dihydrate,Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.148→50 Å / Num. obs: 13247 / % possible obs: 96.4 % / Redundancy: 6.1 % / Net I/σ(I): 9.4
Reflection shellResolution: 3.15→3.2 Å / % possible obs: 65.4 % / Rmerge(I) obs: 0.29 / Rsym value: 0.29

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementStarting model: 2YQ4

2yq4


Resolution: 3.148→41.534 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2922 1303 9.93 %
Rwork0.2045 --
obs0.2133 13121 95.66 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 6.215 Å2 / ksol: 0.279 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6273 Å2-0 Å20 Å2
2---2.9164 Å20 Å2
3---0.2891 Å2
Refinement stepCycle: LAST / Resolution: 3.148→41.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5112 0 88 0 5200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095268
X-RAY DIFFRACTIONf_angle_d1.4397162
X-RAY DIFFRACTIONf_dihedral_angle_d20.2311980
X-RAY DIFFRACTIONf_chiral_restr0.104878
X-RAY DIFFRACTIONf_plane_restr0.006912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1478-3.27370.34641060.2438952X-RAY DIFFRACTION71
3.2737-3.42270.3191370.24311272X-RAY DIFFRACTION94
3.4227-3.6030.32751480.23331335X-RAY DIFFRACTION99
3.603-3.82860.33421480.24411347X-RAY DIFFRACTION99
3.8286-4.1240.33531480.19651337X-RAY DIFFRACTION99
4.124-4.53850.25391530.16261352X-RAY DIFFRACTION99
4.5385-5.19420.25171510.16621372X-RAY DIFFRACTION99
5.1942-6.540.31021500.21921386X-RAY DIFFRACTION99
6.54-41.53760.25351620.21465X-RAY DIFFRACTION99

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