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- PDB-1sev: Mature and translocatable forms of glyoxysomal malate dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 1sev
TitleMature and translocatable forms of glyoxysomal malate dehydrogenase have different activities and stabilities but similar crystal structures
ComponentsMalate dehydrogenase, glyoxysomal precursor
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


glyoxysome / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / glyoxylate cycle / tricarboxylic acid cycle / chloroplast
Similarity search - Function
Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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 ...Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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, glyoxysomal
Similarity search - Component
Biological speciesCitrullus lanatus (watermelon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsCox, B.R. / Chit, M.M. / Weaver, T.M. / Bailey, J. / Gietl, C. / Bell, E. / Banaszak, L.J.
CitationJournal: Febs J. / Year: 2005
Title: Organelle and translocatable forms of glyoxysomal malate dehydrogenase. The effect of the N-terminal presequence
Authors: Cox, B.R. / Chit, M.M. / Weaver, T.M. / Bailey, J. / Gietl, C. / Bell, E. / Banaszak, L.J.
History
DepositionFeb 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
A: Malate dehydrogenase, glyoxysomal precursor
B: Malate dehydrogenase, glyoxysomal precursor


Theoretical massNumber of molelcules
Total (without water)77,0172
Polymers77,0172
Non-polymers00
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-20 kcal/mol
Surface area23470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.800, 96.800, 213.318
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Malate dehydrogenase, glyoxysomal precursor


Mass: 38508.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrullus lanatus (watermelon) / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P19446, malate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 3.86 Å3/Da / Density % sol: 67.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 800, Sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 28, 1998
RadiationMonochromator: Rosenbaum-Rock monochromator #1 high-resolution double-crystal sagittal focusing. Rosenbaum-rock monochromator #2 double crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
X-PLORmodel building
CNS1refinement
HKL-2000data reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MDH

4mdh


Resolution: 2.55→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2577 1674 -RANDOM
Rwork0.2071 ---
all0.21 33912 --
obs0.21 33912 99.8 %-
Displacement parametersBiso mean: 42.7625 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---0.54 Å20 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4620 0 0 293 4913

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