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- PDB-5mdh: CRYSTAL STRUCTURE OF TERNARY COMPLEX OF PORCINE CYTOPLASMIC MALAT... -

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Basic information

Entry
Database: PDB / ID: 5mdh
TitleCRYSTAL STRUCTURE OF TERNARY COMPLEX OF PORCINE CYTOPLASMIC MALATE DEHYDROGENASE ALPHA-KETOMALONATE AND TNAD AT 2.4 ANGSTROMS RESOLUTION
ComponentsMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / (NAD(A)-CHOH(D))
Function / homology
Function and homology information


diiodophenylpyruvate reductase / (2R)-hydroxyphenylpyruvate reductase [NAD(P)H] activity / Malate-aspartate shuttle / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / oxaloacetate metabolic process / : / tricarboxylic acid cycle / NAD binding / cytosol
Similarity search - Function
Malate dehydrogenase, NAD-dependent, cytosolic / Malate dehydrogenase, type 2 / 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 ...Malate dehydrogenase, NAD-dependent, cytosolic / Malate dehydrogenase, type 2 / 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
ALPHA-KETOMALONIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase, cytoplasmic
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChapman, A.D.M. / Cortes, A. / Dafforn, T.R. / Clarke, A.R. / Brady, R.L.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD.
Authors: Chapman, A.D. / Cortes, A. / Dafforn, T.R. / Clarke, A.R. / Brady, R.L.
#1: Journal: Biochemistry / Year: 1989
Title: Refined Crystal Structure of Cytoplasmic Malate Dehydrogenase at 2.5-A Resolution
Authors: Birktoft, J.J. / Rhodes, G. / Banaszak, L.J.
#2: Journal: Biochemistry / Year: 1987
Title: Structure of Porcine Heart Cytoplasmic Malate Dehydrogenase. Combining X-Ray Diffraction and Chemical Sequence Data in Structural Studies
Authors: Birktoft, J.J. / Bradshaw, R.A. / Banaszak, L.J.
#3: Journal: J.Biol.Chem. / Year: 1983
Title: The Presence of a Histidine-Aspartic Acid Pair in the Active Site of 2-Hydroxyacid Dehydrogenases. X-Ray Refinement of Cytoplasmic Malate Dehydrogenase
Authors: Birktoft, J.J. / Banaszak, L.J.
#4: Journal: MOLECULAR STRUCTURE AND BIOLOGICAL ACTIVITY / Year: 1982
Title: The Interactions of Nad/Nadh with 2-Hydroxy Acid Dehydrogenases
Authors: Birktoft, J.J. / Fernley, R.T. / Bradshaw, R.A. / Banaszak, L.J.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Amino Acid Sequence Homology Among the 2-Hydroxy Acid Dehydrogenases. Mitochondrial and Cytoplasmic Malate Dehydrogenases Form a Homologous System with Lactate Dehydrogenase
Authors: Birktoft, J.J. / Fernley, R.T. / Bradshaw, R.A. / Banaszak, L.J.
#6: Journal: STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN
Year: 1975
Title: Nicotinamide Adenine Dinucleotide and the Active Site of Cytoplasmic Malate Dehydrogenase
Authors: Banaszak, L.J. / Webb, L.E.
#7: Journal: Biochemistry / Year: 1973
Title: Conformation of Nicotinamide Adenine Dinucleotide Bound to Cytoplasmic Malate Dehydrogenase
Authors: Webb, L.E. / Hill, E.J. / Banaszak, L.J.
#8: Journal: J.Mol.Biol. / Year: 1972
Title: Polypeptide Conformation of Cytoplasmic Malate Dehydrogenase from an Electron Density Map at 3.0 Angstroms Resolution
Authors: Hill, E. / Tsernoglou, D. / Webb, L. / Banaszak, L.J.
#9: Journal: Biochem.Biophys.Res.Commun. / Year: 1972
Title: The Identification of an Asymmetric Complex of Nicotinamide Adenine Dinucleotide and Pig Heart Cytoplasmic Malate Dehydrogenase
Authors: Glatthaar, B.E. / Banaszak, L.J. / Bradshaw, R.A.
#10: Journal: J.Mol.Biol. / Year: 1972
Title: Cytoplasmic Malate Dehydrogenase--Heavy Atom Derivatives and Low Resolution Structure
Authors: Tsernoglou, D. / Hill, E. / Banaszak, L.J.
#11: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: Structural Studies on Heart Muscle Malate Dehydrogenases
Authors: Tsernoglou, D. / Hill, E. / Banaszak, L.J.
History
DepositionOct 8, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 17, 2011Group: Derived calculations
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALATE DEHYDROGENASE
B: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2996
Polymers72,7362
Non-polymers1,5634
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-40 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.700, 144.432, 59.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO SUBUNITS WHICH HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *B*. ALTHOUGH THE TWO SUBUNITS ARE CHEMICALLY EQUIVALENT, THEY ARE RELATED BY A NON-CRYSTALLOGRAPHIC SYMMETRY AXIS WITH A ROTATION ANGLE OF 174.9 DEGREES WHICH IS SIGNIFICANTLY DIFFERENT FROM A TRUE TWO-FOLD SYMMETRY OPERATION.

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Components

#1: Protein MALATE DEHYDROGENASE


Mass: 36367.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Tissue: MUSCLE / Cellular location: CYTOPLASM / Organ: HEART / Production host: Escherichia coli (E. coli) / References: UniProt: P11708, malate 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-MAK / ALPHA-KETOMALONIC ACID


Mass: 118.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 57.1 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.15 mMammonium acetate1reservoir
216 %(v/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 26268 / % possible obs: 89.3 % / Observed criterion σ(I): 0 / Redundancy: 3.96 % / Biso Wilson estimate: 42.44 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 12.34
Reflection shellResolution: 2.4→2.51 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.72 / Rsym value: 0.32 / % possible all: 91.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MDH

4mdh


Resolution: 2.4→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.67 / ESU R Free: 0.3
Details: ATOMS WITH ZERO OCCUPANCIES HAVE NO ELECTRON DENSITY IN THE MAPS, THEREFORE THE POSITIONS OF THESE RESIDUES CANNOT BE DETERMINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1492 5 %RANDOM
Rwork0.1994 ---
obs-29520 84.3 %-
Displacement parametersBiso mean: 46.38 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5100 0 104 354 5558
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0650.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3162
X-RAY DIFFRACTIONp_mcangle_it2.1193
X-RAY DIFFRACTIONp_scbond_it1.4292
X-RAY DIFFRACTIONp_scangle_it2.1733
X-RAY DIFFRACTIONp_plane_restr0.022
X-RAY DIFFRACTIONp_chiral_restr0.128
X-RAY DIFFRACTIONp_singtor_nbd0.1880.3
X-RAY DIFFRACTIONp_multtor_nbd0.2560.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1890.3
X-RAY DIFFRACTIONp_planar_tor7.87
X-RAY DIFFRACTIONp_staggered_tor20.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.420
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199 / Rfactor Rfree: 0.25378 / Rfactor Rwork: 0.19946
Solvent computation
*PLUS
Displacement parameters
*PLUS

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