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- PDB-1ldm: Refined crystal structure of dogfish M4 apo-lactate dehydrogenase -

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Entry
Database: PDB / ID: 1ldm
TitleRefined crystal structure of dogfish M4 apo-lactate dehydrogenase
ComponentsM4 LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / cytoplasm
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / 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 ...L-lactate dehydrogenase / L-lactate dehydrogenase active site. / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / OXAMIC ACID / L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesSqualus acanthias (spiny dogfish)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsGriffith, J.P. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1987
Title: Refined crystal structure of dogfish M4 apo-lactate dehydrogenase.
Authors: Abad-Zapatero, C. / Griffith, J.P. / Sussman, J.L. / Rossmann, M.G.
#1: Journal: J.Mol.Biol. / Year: 1976
Title: A Comparison of the Structures of Apo Dogfish M4 Lactate Dehydrogenase and its Ternary Complexes
Authors: White, J.L. / Hackert, M.L. / Buehner, M. / Adams, M.J. / Ford, G.C. / Lentzjunior, P.J. / Smiley, I.E. / Steindel, S.J. / Rossmann, M.G.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1977
Title: Structural Adaptations of Lactate Dehydrogenase Isozymes
Authors: Eventoff, W. / Rossmann, M.G. / Taylor, S.S. / Torff, H.-J. / Meyer, H. / Keil, W. / Kiltz, H.-H.
#3: Journal: J.Mol.Biol. / Year: 1975
Title: A 5 Angstroms X-Ray Diffraction Study of Coenzyme-Deficient Lactate Dehydrogenase,Nad-Pyruvate Ternary Complex
Authors: White, J. / Rossmann, M.G. / Ford, G.C.
#4: Journal: Isozymes-Molecular Structure / Year: 1975
Title: A Structural Comparison of Porcine B4 and Dogfish A4 Isozymes of Lactate Dehydrogenase
Authors: Eventoff, W. / Hackert, M.L. / Steindel, S.J. / Rossmann, M.G.
#5: Journal: The Enzymes,Third Edition / Year: 1975
Title: Lactate Dehydrogenase
Authors: Holbrook, J.J. / Liljas, A. / Steindel, S.J. / Rossmann, M.G.
#6: Journal: Annu.Rev.Biochem. / Year: 1974
Title: X-Ray Studies of Protein Interactions
Authors: Liljas, A. / Rossmann, M.G.
#7: Journal: Nature / Year: 1974
Title: Chemical and Biological Evolution of a Nucleotide Binding Protein
Authors: Rossmann, M.G. / Moras, D. / Olsen, K.W.
#8: Journal: J.Mol.Biol. / Year: 1974
Title: Recognition of Structural Domains in Globular Proteins
Authors: Rossmann, M.G. / Liljas, A.
#9: Journal: Biochem.Biophys.Res.Commun. / Year: 1973
Title: Atomic Co-Ordinates for Dogfish M4 Apo-Lactate Dehydrogenase
Authors: Adams, M.J. / Ford, G.C. / Liljas, A. / Rossmann, M.G.
#10: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: Structure-Function Relationships in Lactate Dehydrogenase
Authors: Adams, M.J. / Buehner, M. / Chandrasekhar, K. / Ford, G.C. / Hackert, M.L. / Liljas, A. / Rossmann, M.G. / Smiley, I.E. / Allison, W.S. / Everse, J. / Kaplan, N.O. / Taylor, S.S.
#11: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: Amino-Acid Sequence of Dogfish M4 Lactate Dehydrogenase
Authors: Taylor, S.S. / Oxley, S.S. / Allison, W.S. / Kaplan, N.O.
#12: Journal: J.Mol.Biol. / Year: 1973
Title: Molecular Symmetry Axes and Subunit Interfaces in Certain Dehydrogenases
Authors: Rossmann, M.G. / Adams, M.J. / Buehner, M. / Ford, G.C. / Hackert, M.L. / Liljas, A. / Rao, S.T. / Banaszak, L.J. / Hill, E. / Tsernoglou, D. / Webb, L.
#13: Journal: J.Mol.Biol. / Year: 1973
Title: Functional Anion Binding Sites in Dogfish M4 Lactate Dehydrogenase
Authors: Adams, M.J. / Liljas, A. / Rossmann, M.G.
#14: Journal: J.Mol.Biol. / Year: 1973
Title: Binding of Oxamate to the Apoenzyme of Dogfish M4 Lactate Dehydrogenase
Authors: Mcphersonjunior, A.
#15: Journal: J.Mol.Biol. / Year: 1973
Title: Conformation of Coenzyme Fragments When Bound to Lactate Dehydrogenase
Authors: Chandrasekhar, K. / Mcphersonjunior, A. / Adams, M.J. / Rossmann, M.G.
#16: Journal: J.Mol.Biol. / Year: 1971
Title: The 5 Angstroms Resolution Structure of an Abortive Ternary Complex of Lactate Dehydrogenase and its Comparison with the Apo-Enzyme
Authors: Smiley, I.E. / Koekoek, R. / Adams, M.J. / Rossmann, M.G.
#17: Journal: Nature / Year: 1970
Title: Structure of Lactate Dehydrogenase at 2.8 Angstroms Resolution
Authors: Adams, M.J. / Ford, G.C. / Koekoek, R. / Lentzjunior, P.J. / Mcphersonjunior, A. / Rossmann, M.G. / Smiley, I.E. / Schevitz, R.W. / Wonacott, A.J.
#18: Journal: J.Mol.Biol. / Year: 1969
Title: Low Resolution Study of Crystalline L-Lactate Dehydrogenase
Authors: Adams, M.J. / Haas, D.J. / Jeffery, B.A. / Mcphersonjunior, A. / Mermall, H.L. / Rossmann, M.G. / Schevitz, R.W. / Wonacott, A.J.
#19: Journal: Proc.Natl.Acad.Sci.USA / Year: 1967
Title: The Crystal Structure of Lactic Dehydrogenase
Authors: Rossmann, M.G. / Jeffery, B.A. / Main, P. / Warren, S.
History
DepositionNov 25, 1987Processing site: BNL
Revision 1.0Jul 12, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2013Group: Derived calculations / Other
Revision 1.4Oct 22, 2014Group: Derived calculations / Structure summary
Revision 1.5Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details / _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: M4 LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1694
Polymers36,3271
Non-polymers8423
Water4,414245
1
A: M4 LACTATE DEHYDROGENASE
hetero molecules

A: M4 LACTATE DEHYDROGENASE
hetero molecules

A: M4 LACTATE DEHYDROGENASE
hetero molecules

A: M4 LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,67516
Polymers145,3094
Non-polymers3,36612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
4
A: M4 LACTATE DEHYDROGENASE
hetero molecules


  • crystal asymmetric unit, crystal frame
  • 37.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)37,1694
Polymers36,3271
Non-polymers8423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
Unit cell
Length a, b, c (Å)134.500, 134.500, 85.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MC4212
Atom site foot note1: RESIDUE PRO 139 IS A CIS PROLINE.
SymmetryPoint symmetry: (Schoenflies symbol: D2 (2x2 fold dihedral))
DetailsNON-CRYSTALLOGRAPHIC SYMMETRY ELEMENTS CORRESPONDING TO THE THREE ORTHOGONAL MOLECULAR SYMMETRY AXES ARE PRESENTED ON THE *MTRIX* RECORDS BELOW.

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Components

#1: Protein M4 LACTATE DEHYDROGENASE


Mass: 36327.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Squalus acanthias (spiny dogfish) / References: UniProt: P00341, L-lactate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUES IN THIS ENTRY ARE NUMBERED SEQUENTIALLY FROM 1 - 329. SEE THE PAPER CITED AS REFERENCE ...THE RESIDUES IN THIS ENTRY ARE NUMBERED SEQUENTIALLY FROM 1 - 329. SEE THE PAPER CITED AS REFERENCE 1 ABOVE FOR AN EXPLANATION OF THE NUMBERING SYSTEM USED IN SOME EARLIER LDH ENTRIES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: referred to 'Pesca, A. J.', (1967) J.Biol.Chem., 242, 2151-2167
Components of the solutions
*PLUS
Conc.: 30 %sat / Common name: ammonium sulfate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.1→6 Å / Rfactor obs: 0.173
Details: SPACE GROUP C 4 21 2 (WHICH, MORE PROPERLY, SHOULD BE NAMED C 4 2 21) IS A NON-STANDARD REPRESENTATION OF SPACE GROUP P 4 21 2. IN THIS CASE THE AXES OF THE UNIT CELL ARE CONSIDERED TO BE LEFT-HANDED.
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 56 245 2843
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.03
X-RAY DIFFRACTIONp_angle_d0.0480.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.2130.5
X-RAY DIFFRACTIONp_multtor_nbd0.2670.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.260.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 6 Å / σ(I): 2 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS

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