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- PDB-1mld: REFINED STRUCTURE OF MITOCHONDRIAL MALATE DEHYDROGENASE FROM PORC... -

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Basic information

Entry
Database: PDB / ID: 1mld
TitleREFINED STRUCTURE OF MITOCHONDRIAL MALATE DEHYDROGENASE FROM PORCINE HEART AND THE CONSENSUS STRUCTURE FOR DICARBOXYLIC ACID OXIDOREDUCTASES
ComponentsMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE(NAD(A)-CHOH(D))
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / tricarboxylic acid cycle / aerobic respiration / protein-folding chaperone binding / mitochondrial matrix / protein homodimerization activity / mitochondrion / cytoplasm
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
CITRIC ACID / Malate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.83 Å
AuthorsGleason, W.B. / Fu, Z. / Birktoft, J.J. / Banaszak, L.J.
Citation
Journal: Biochemistry / Year: 1994
Title: Refined crystal structure of mitochondrial malate dehydrogenase from porcine heart and the consensus structure for dicarboxylic acid oxidoreductases.
Authors: Gleason, W.B. / Fu, Z. / Birktoft, J. / Banaszak, L.
#1: Journal: Biochemistry / Year: 1993
Title: Determinants of Protein Thermostability Observed in the 1.9 Angstrom Crystal Structure of Malate Dehydrogenase from the Thermophilic Bacterium Thermus Flavus
Authors: Kelly, C.A. / Nishiyama, M. / Ohnishi, Y. / Beppu, T. / Birktoft, J.J.
#2: Journal: Biochemistry / Year: 1989
Title: Refined Crystal Structure of Cytoplasmic Malate Dehydrogenase at 2.5 Angstroms Resolution
Authors: Birktoft, J.J. / Rhodes, G. / Banaszak, L.J.
#3: Journal: Biochem.Soc.Trans. / Year: 1989
Title: Comparison of the Molecular Structures of Cytoplasmic and Mitochondrial Malate Dehydrogenases
Authors: Birktoft, J.J. / Fu, Z. / Carnahan, G.E. / Rodes, G. / Roderick, S.L. / Banaszak, L.J.
#4: Journal: J.Biol.Chem. / Year: 1986
Title: The Three Dimensional Structure of Porcine Heart Mitochondrial Malate Dehydrogenase at 3.0 Angstrom Resolution
Authors: Roderick, S.L. / Banaszak, L.J.
History
DepositionJan 24, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: MALATE DEHYDROGENASE
B: MALATE DEHYDROGENASE
C: MALATE DEHYDROGENASE
D: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,2518
Polymers132,4824
Non-polymers7684
Water9,386521
1
A: MALATE DEHYDROGENASE
B: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6254
Polymers66,2412
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-16 kcal/mol
Surface area22360 Å2
MethodPISA
2
C: MALATE DEHYDROGENASE
D: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6254
Polymers66,2412
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-16 kcal/mol
Surface area22290 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9510 Å2
ΔGint-42 kcal/mol
Surface area42990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.750, 146.760, 67.580
Angle α, β, γ (deg.)90.00, 108.16, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 119 / 2: CIS PROLINE - PRO A 190 / 3: CIS PROLINE - PRO B 119 / 4: CIS PROLINE - PRO B 190 / 5: CIS PROLINE - PRO C 119 / 6: CIS PROLINE - PRO C 190 / 7: CIS PROLINE - PRO D 119 / 8: CIS PROLINE - PRO D 190

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Components

#1: Protein
MALATE DEHYDROGENASE


Mass: 33120.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00346, malate dehydrogenase
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal grow
*PLUS
pH: 5.8 / Method: unknown
Details: referred to 'Roderick, S.L.', (1986) J.Biol.Chem., 261, 9461-9464
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1PEG600011
2citrate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.83 Å / Num. obs: 91000 / Rmerge(I) obs: 0.145

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.83→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.211 -
obs0.211 83454
Refinement stepCycle: LAST / Resolution: 1.83→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9240 0 52 521 9813
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.211 / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.2

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