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- PDB-2ldx: CHARACTERIZATION OF THE ANTIGENIC SITES ON THE REFINED 3-ANGSTROM... -

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Basic information

Entry
Database: PDB / ID: 2ldx
TitleCHARACTERIZATION OF THE ANTIGENIC SITES ON THE REFINED 3-ANGSTROMS RESOLUTION STRUCTURE OF MOUSE TESTICULAR LACTATE DEHYDROGENASE C4
ComponentsAPO-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE(CHOH(D)-NAD(A))
Function / homology
Function and homology information


lactate biosynthetic process from pyruvate / Pyruvate metabolism / pyruvate catabolic process / L-lactate dehydrogenase / ATP biosynthetic process / flagellated sperm motility / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / motile cilium / cilium ...lactate biosynthetic process from pyruvate / Pyruvate metabolism / pyruvate catabolic process / L-lactate dehydrogenase / ATP biosynthetic process / flagellated sperm motility / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / motile cilium / cilium / cytoplasm / cytosol
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
L-lactate dehydrogenase C chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.96 Å
AuthorsGriffith, J.P. / Rossmann, M.G.
Citation
Journal: J.Biol.Chem. / Year: 1987
Title: Characterization of the antigenic sites on the refined 3-A resolution structure of mouse testicular lactate dehydrogenase C4.
Authors: Hogrefe, H.H. / Griffith, J.P. / Rossmann, M.G. / Goldberg, E.
#1: Journal: J.Biol.Chem. / Year: 1979
Title: The Structure of Mouse Testicular Lactate Dehydrogenase Isoenzyme C4 at 2.9 Angstroms Resolution
Authors: Musick, W.D.L. / Rossmann, M.G.
#2: Journal: J.Mol.Biol. / Year: 1976
Title: A Low-Resolution Study of Testicular Lactate Dehydrogenase Using the Molecular Replacement Technique
Authors: Musick, W.D.L. / Adams, A.D. / Rossmann, M.G. / Wheat, T.E. / Goldberg, E.
#3: Journal: J.Mol.Biol. / Year: 1973
Title: A Crystalline Form of Testes-Specific Lactate Dehydrogenase
Authors: Adams, A.D. / Adams, M.J. / Rossmann, M.G.
History
DepositionNov 25, 1987Processing site: BNL
SupersessionApr 19, 1989ID: 1LDX
Revision 1.0Apr 19, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_status / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_ncs_oper / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _pdbx_database_status.process_site / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ref_seq_dif.details
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Refinement description / Category: chem_comp_atom / chem_comp_bond / struct_ncs_oper
Item: _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] ..._struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3]

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: APO-LACTATE DEHYDROGENASE
B: APO-LACTATE DEHYDROGENASE
C: APO-LACTATE DEHYDROGENASE
D: APO-LACTATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)143,4664
Polymers143,4664
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19540 Å2
ΔGint-138 kcal/mol
Surface area46680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.800, 76.600, 63.900
Angle α, β, γ (deg.)109.70, 89.50, 96.50
Int Tables number1
Space group name H-MP1
Atom site foot note1: RESIDUE PRO 138 IS A CIS-PROLINE.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(0.97259642, 0.22474897, 0.0625019), (0.22298103, -0.97459452, 0.00706517), (0.06306138, 0.00718494, -0.99800189)
2given(-0.97260396, -0.22350424, -0.06666712), (-0.22198939, 0.81104902, 0.54020195), (-0.06638902, 0.54161952, -0.83844506)
3given(-0.99999245, -0.00124473, 0.00416522), (-0.00099165, -0.8364545, -0.54726712), (0.00332765, -0.54880445, 0.83644695)

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Components

#1: Protein
APO-LACTATE DEHYDROGENASE


Mass: 35866.605 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P00342, L-lactate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SECONDARY STRUCTURE SPECIFICATIONS ARE THOSE PRODUCED BY PROGRAM *DSSP* OF W. KABSCH AND C. SANDER.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: microdialysis / Details: seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.02 MTris-HCl11
240 %satammonium sulfate12

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Data collection

Reflection
*PLUS
Highest resolution: 2.96 Å / Lowest resolution: 10 Å / % possible obs: 0.66 % / Num. measured all: 20475 / Rmerge(I) obs: 0.254

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.96→10 Å / Rfactor obs: 0.256
Refinement stepCycle: LAST / Resolution: 2.96→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10060 0 0 31 10091
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.03
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.51
X-RAY DIFFRACTIONp_mcangle_it0.2521.5
X-RAY DIFFRACTIONp_scbond_it0.9351
X-RAY DIFFRACTIONp_scangle_it0.5391.5
X-RAY DIFFRACTIONp_plane_restr0.0190.02
X-RAY DIFFRACTIONp_chiral_restr0.1430.15
X-RAY DIFFRACTIONp_singtor_nbd0.2140.5
X-RAY DIFFRACTIONp_multtor_nbd0.2130.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2520.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.43
X-RAY DIFFRACTIONp_staggered_tor24.715
X-RAY DIFFRACTIONp_orthonormal_tor31.420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.96 Å / Lowest resolution: 10 Å / Rfactor obs: 0.256
Solvent computation
*PLUS
Displacement parameters
*PLUS

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