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- PDB-1hye: CRYSTAL STRUCTURE OF THE MJ0490 GENE PRODUCT, THE FAMILY OF LACTA... -

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Basic information

Entry
Database: PDB / ID: 1hye
TitleCRYSTAL STRUCTURE OF THE MJ0490 GENE PRODUCT, THE FAMILY OF LACTATE/MALATE DEHYDROGENASE, DIMERIC STRUCTURE
ComponentsL-LACTATE/MALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / nucleotide binding domain
Function / homology
Function and homology information


L-2-hydroxycarboxylate dehydrogenase [NAD(P)+] / L-2-hydroxycarboxylate dehydrogenase (NAD+) activity / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain ...L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsLee, B.I. / Chang, C. / Cho, S.-J. / Suh, S.W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the MJ0490 gene product of the hyperthermophilic archaebacterium Methanococcus jannaschii, a novel member of the lactate/malate family of dehydrogenases.
Authors: Lee, B.I. / Chang, C. / Cho, S.J. / Eom, S.H. / Kim, K.K. / Yu, Y.G. / Suh, S.W.
History
DepositionJan 19, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 21, 2018Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rsym_value
Revision 1.4Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-LACTATE/MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4022
Polymers34,6581
Non-polymers7431
Water1,35175
1
A: L-LACTATE/MALATE DEHYDROGENASE
hetero molecules

A: L-LACTATE/MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8034
Polymers69,3162
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)47.647, 125.101, 58.082
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe assembly is a dimer generated from the monomer in the asymmetric unit by the operations : -x, -y, z.

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Components

#1: Protein L-LACTATE/MALATE DEHYDROGENASE


Mass: 34658.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0490 / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q60176, L-lactate dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2-methyl-2,4-pentanediol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 287 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mg/mlprotein1drop
2150 mM1dropNaCl
320 mMTris-HCl1drop
410 mM1dropMgCl2
51.0 mMPMSF1drop
618 mMdetergent1reservoir
70.1 MMES-NaOH1reservoir
810 %mPEG3501reservoir
912 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 10, 1998 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 28196 / Num. obs: 26843 / % possible obs: 95.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 1103 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.5 / % possible all: 80
Reflection
*PLUS
Num. measured all: 113866
Reflection shell
*PLUS
% possible obs: 80 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementStarting model: PDB ENTRY 1a5z

1a5z


Resolution: 1.9→19.49 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 253181.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2394 9.9 %RANDOM
Rwork0.194 ---
obs0.194 24219 86 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.69 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.27 Å20 Å20 Å2
2---1.67 Å20 Å2
3----3.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 48 76 2507
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d1.46
X-RAY DIFFRACTIONc_mcbond_it2.621.5
X-RAY DIFFRACTIONc_mcangle_it3.62
X-RAY DIFFRACTIONc_scbond_it4.462
X-RAY DIFFRACTIONc_scangle_it6.352.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 305 10.2 %
Rwork0.252 2676 -
obs--65.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3REFINEREFINE
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.46

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