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- PDB-3kb6: Crystal structure of D-Lactate dehydrogenase from aquifex aeolicu... -

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Basic information

Entry
Database: PDB / ID: 3kb6
TitleCrystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid
ComponentsD-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / D-LDH / NAD / STRUCTURAL GENOMICS / NPPSFA / NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI
Function / homology
Function and homology information


serine family amino acid biosynthetic process / (S)-2-hydroxyglutarate dehydrogenase activity / phosphoglycerate dehydrogenase activity / D-lactate dehydrogenase (NAD+) activity / NAD binding
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 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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
LACTIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / PROPANOIC ACID / D-lactate dehydrogenase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 Å
AuthorsAntonyuk, S.V. / Strange, R.W. / Ellis, M.J. / Bessho, Y. / Kuramitsu, S. / Yokoyama, S. / Hasnain, S.S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate).
Authors: Antonyuk, S.V. / Strange, R.W. / Ellis, M.J. / Bessho, Y. / Kuramitsu, S. / Inoue, Y. / Yokoyama, S. / Hasnain, S.S.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionNov 10, 2009ID: 2PI1
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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
C: D-lactate dehydrogenase
D: D-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,19946
Polymers153,8344
Non-polymers7,36542
Water15,367853
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26150 Å2
ΔGint-100 kcal/mol
Surface area51230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.938, 94.432, 188.849
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
D-lactate dehydrogenase


Mass: 38458.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_727, ldhA / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA834(DE3) / References: UniProt: O66939, D-lactate dehydrogenase

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Non-polymers , 7 types, 895 molecules

#2: Chemical
ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H6O2
#3: Chemical
ChemComp-LAC / LACTIC ACID


Mass: 90.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H6O3
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 853 / 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: 2.64 Å3/Da / Density % sol: 53.33 % / Mosaicity: 0.386 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 25% PEG 200, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2007 / Details: MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.12→38 Å / Num. obs: 88902 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.088 / Χ2: 1.206 / Net I/σ(I): 12.2
Reflection shellResolution: 2.12→2.2 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 5.3 / Num. unique all: 7005 / Χ2: 1.207 / % possible all: 76.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DLD

2dld


Resolution: 2.12→38 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.323 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.212 4439 5 %RANDOM
Rwork0.164 ---
obs0.167 88512 95.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.88 Å2 / Biso mean: 29.453 Å2 / Biso min: 9.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å2-0 Å2
2--3.13 Å2-0 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 2.12→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10697 0 452 853 12002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02211426
X-RAY DIFFRACTIONr_bond_other_d0.0020.028036
X-RAY DIFFRACTIONr_angle_refined_deg1.4942.02615358
X-RAY DIFFRACTIONr_angle_other_deg0.8953.00119713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96351371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6924.156462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.287152200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.891567
X-RAY DIFFRACTIONr_chiral_restr0.0870.21782
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022107
X-RAY DIFFRACTIONr_mcbond_it0.7631.56697
X-RAY DIFFRACTIONr_mcbond_other0.1981.52722
X-RAY DIFFRACTIONr_mcangle_it1.429210926
X-RAY DIFFRACTIONr_scbond_it2.34734729
X-RAY DIFFRACTIONr_scangle_it3.7494.54412
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 257 -
Rwork0.21 4865 -
all-5122 -
obs--75.75 %

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