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- PDB-2d4a: Structure of the malate dehydrogenase from Aeropyrum pernix -

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Basic information

Entry
Database: PDB / ID: 2d4a
TitleStructure of the malate dehydrogenase from Aeropyrum pernix
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / malate dehydrogenase / archaea / hyperthermophile
Function / homology
Function and homology information


malate dehydrogenase [NAD(P)+] / carboxylic acid metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / tricarboxylic acid cycle / carbohydrate metabolic process
Similarity search - Function
Malate dehydrogenase, type 3 / 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 ...Malate dehydrogenase, type 3 / 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
Malate dehydrogenase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.87 Å
AuthorsKawakami, R. / Sakuraba, H. / Tsuge, H. / Ohshima, T.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Refolding, characterization and crystal structure of (S)-malate dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix.
Authors: Kawakami, R. / Sakuraba, H. / Goda, S. / Tsuge, H. / Ohshima, T.
History
DepositionOct 12, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Malate dehydrogenase
D: Malate dehydrogenase
C: Malate dehydrogenase
A: Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)134,1154
Polymers134,1154
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13020 Å2
ΔGint-81 kcal/mol
Surface area41380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.168, 84.012, 216.148
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
Malate dehydrogenase


Mass: 33528.828 Da / Num. of mol.: 4 / Fragment: residues 1-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YEA1, malate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.6 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 40% PEG600, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.87→19.92 Å / Num. all: 33382 / Num. obs: 33305 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.87→2.97 Å / % possible all: 99

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Processing

Software
NameVersionClassification
crystalcleardata collection
HKL-2000data reduction
SOLVEphasing
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.87→19.92 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.24 2707 RANDOM
Rwork0.2053 --
all0.20877 33382 -
obs0.2053 27218 -
Refinement stepCycle: LAST / Resolution: 2.87→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9171 0 0 121 9292

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