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- PDB-1j49: INSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS... -

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Basic information

Entry
Database: PDB / ID: 1j49
TitleINSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS OF D-LACTATE DEHYDROGENASE FROM LACTOBACILLUS BULGARICUS
ComponentsD-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD-DEPENDENT DEHYDROGENASE / LAST STEP OF GLYCOLYSIS UNDER ANAEROBIC CONDITIONS / REVERSIBLE INTERCONVERSION OF PYRUVATE INTO D-LACTATE
Function / homology
Function and homology information


D-lactate dehydrogenase / D-lactate dehydrogenase (NAD+) activity / lactate metabolic process / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / D-lactate dehydrogenase
Similarity search - Component
Biological speciesLactobacillus delbrueckii subsp. bulgaricus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRazeto, A. / Kochhar, S. / Hottinger, H. / Dauter, M. / Wilson, K.S. / Lamzin, V.S.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus.
Authors: Razeto, A. / Kochhar, S. / Hottinger, H. / Dauter, M. / Wilson, K.S. / Lamzin, V.S.
History
DepositionAug 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The authors maintain that their sequence is correct. The density for these residues ...SEQUENCE The authors maintain that their sequence is correct. The density for these residues suggests ILE59, ARG117, AND VAL152 instead of those in the database reference match.

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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)75,6655
Polymers74,2422
Non-polymers1,4233
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-59 kcal/mol
Surface area25340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.4, 79.4, 228.5
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.31073, -0.06203, 0.94847), (0.09671, -0.99475, -0.03337), (0.94557, 0.08136, 0.3151)
Vector: -1.19188, 54.584, -0.08465)

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Components

#1: Protein D-LACTATE DEHYDROGENASE / D-LDH


Mass: 37121.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus (bacteria)
Species: Lactobacillus delbrueckii / Strain: N42
Description: NESTLE CULTURE COLLECTION. PCR AMPLIFIED LDHA GENE
Cellular location: CYTOPLASM / Gene: LDHA / Plasmid: PKBULDH / Cellular location (production host): CYTOPLASM / Gene (production host): LDHA / Production host: Escherichia coli (E. coli) / Strain (production host): SURE / References: UniProt: P26297, D-lactate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 %PEG2000 Me1reservoir
20.2 Mammonium sulfate1reservoir
35 mMNADH1reservoir
40.1 Msodium acetate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.916
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1994 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 38147 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.82 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.73 / % possible all: 93.3
Reflection
*PLUS
Lowest resolution: 15 Å / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 93.3 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DLD

2dld


Resolution: 2.2→15 Å / SU B: 4.35 / SU ML: 0.11
Cross valid method: THROUGHOUT (EXCEPT FOR THE LAST 2 REFINEMENT CYCLES)
σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.24
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1884 5 %RANDOM
Rwork0.207 ---
obs0.209 37544 98.7 %-
Displacement parametersBiso mean: 44.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5207 0 93 279 5579
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.015
X-RAY DIFFRACTIONp_angle_d0.0250.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.81
X-RAY DIFFRACTIONp_mcangle_it1.51.5
X-RAY DIFFRACTIONp_scbond_it0.81
X-RAY DIFFRACTIONp_scangle_it1.41.5
X-RAY DIFFRACTIONp_plane_restr0.0260.03
X-RAY DIFFRACTIONp_chiral_restr0.030.05
X-RAY DIFFRACTIONp_singtor_nbd0.20.2
X-RAY DIFFRACTIONp_multtor_nbd0.30.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.231
X-RAY DIFFRACTIONp_xyhbond_nbd0.231
X-RAY DIFFRACTIONp_planar_tor4.37
X-RAY DIFFRACTIONp_staggered_tor18.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor35.620
X-RAY DIFFRACTIONp_special_tor015
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.209 / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS

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