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- PDB-1llc: STRUCTURE DETERMINATION OF THE ALLOSTERIC L-LACTATE DEHYDROGENASE... -

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Entry
Database: PDB / ID: 1llc
TitleSTRUCTURE DETERMINATION OF THE ALLOSTERIC L-LACTATE DEHYDROGENASE FROM LACTOBACILLUS CASEI AT 3.0 ANGSTROMS RESOLUTION
ComponentsL-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE(CHOH(D)-NAD(A))
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / glycolytic 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
1,6-di-O-phosphono-alpha-D-fructofuranose / L-lactate dehydrogenase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsBuehner, M. / Hecht, H.J. / Hensel, R.
Citation
Journal: Acta Crystallogr.,Sect.A / Year: 1984
Title: STRUCTURE DETERMINATION OF THE ALLOSTERIC L-LACTATE DEHYDROGENASE FROM LACTOBACILLUS-CASEI AT 3A RESOLUTION.
Authors: Buehner, M. / Hecht, H.J.
#1: Journal: Z.Kristallogr. / Year: 1987
Title: Die Strukturbestimmung Der Allosterischen L-Laktat-Dehydrogenase Aus Lactobacillus Casei Mittels Molekularem Ersatz. Phasenexpansion Und Phasenverfeinerung Mittels Nichtkristallographischer Symmetrie (German)
Authors: Buehner, M. / Hecht, H.J.
#2: Journal: Eur.J.Biochem. / Year: 1983
Title: The Complete Primary Structure of the Allosteric L-Lactate Dehydrogenase from Lactobacillus Casei
Authors: Hensel, R. / Mayr, U. / Yang, C.
#3: Journal: J.Mol.Biol. / Year: 1982
Title: Crystallization and Preliminary Crystallographic Analysis at Low Resolution of the Allosteric L-Lactate Dehydrogenase from Lactobacillus Casei
Authors: Buehner, M. / Hecht, H.-J. / Hensel, R. / Mayr, U.
History
DepositionNov 21, 1988Processing site: BNL
Revision 1.0Jul 12, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Jul 26, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / cell / chem_comp / database_2 / database_PDB_matrix / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_ncs_oper
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][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] / _cell.Z_PDB / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _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][2] / _database_PDB_matrix.origx[3][3] / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.oper_expression / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_planes.rmsd / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Aug 2, 2023Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.assembly_id
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET SHEET S2 CONTAINS A BIFURCATED STRAND. THIS IS REPRESENTED ON THE *SHEET* RECORDS BELOW BY ...SHEET SHEET S2 CONTAINS A BIFURCATED STRAND. THIS IS REPRESENTED ON THE *SHEET* RECORDS BELOW BY PRESENTING TWO SHEETS (S2A AND S2B) THAT DIFFER ONLY IN ONE STRAND.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9163
Polymers35,4791
Non-polymers4362
Water00
1
A: L-LACTATE DEHYDROGENASE
hetero molecules

A: L-LACTATE DEHYDROGENASE
hetero molecules

A: L-LACTATE DEHYDROGENASE
hetero molecules

A: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,66212
Polymers141,9174
Non-polymers1,7458
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
point symmetry operation2
2
A: L-LACTATE DEHYDROGENASE
hetero molecules

A: L-LACTATE DEHYDROGENASE
hetero molecules

A: L-LACTATE DEHYDROGENASE
hetero molecules

A: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,66212
Polymers141,9174
Non-polymers1,7458
Water0
TypeNameSymmetry operationNumber
point symmetry operation4
Unit cell
Length a, b, c (Å)169.200, 85.380, 180.180
Angle α, β, γ (deg.)90.00, 91.30, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUE 141 IS A CIS PROLINE. / 2: SEE REMARK 8.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.39602671, -0.91816381), (-1), (-0.91831418, -0.39602671)
3generate(-0.59264499, 0.80488991, -0.03115019), (-0.8054149, -0.59176878, 0.03255789), (0.00773546, 0.044493, 0.99897263)43.18003, 12.07871, 121.07681
4generate(0.59264499, 0.80488991, 0.03115019), (0.8054149, -0.59176878, -0.03255789), (-0.00773546, 0.044493, -0.99897263)43.18003, 12.07871, 121.07681
5generate(-0.20609758, -0.80488991, 0.55648149), (-0.34886418, 0.59176878, 0.72660902), (-0.91430729, -0.044493, -0.40272226)43.18003, 12.07871, 121.07681
6generate(0.20609758, -0.80488991, -0.55648149), (0.34886418, 0.59176878, -0.72660902), (0.91430729, -0.044493, 0.40272226)43.18003, 12.07871, 121.07681
DetailsIN SOLUTION AS WELL AS IN THE CRYSTAL, THE MOLECULE CONSISTS OF A TETRAMER (FOUR SUBUNITS OF IDENTICAL SEQUENCE). THERE ARE TWO CRYSTALLOGRAPHICALLY INDEPENDENT MOLECULES IN THE CRYSTAL. ONE TETRAMER (CALLED *CENTRAL*) SITS ON A CRYSTALLOGRAPHIC TW0-FOLD AXIS AND A SECOND TETRAMER (CALLED *PERIPHERAL*) SITS IN A GENERAL POSITION. THE ASYMMETRIC UNIT, THEREFORE, CONSISTS OF TWO SUBUNITS FROM THE *CENTRAL* MOLECULE AND ALL FOUR SUBUNITS FROM THE *PERIPHERAL* MOLECULE. THE THREE TRANSFORMATIONS PRESENTED ON *MTRIX* RECORDS BELOW WILL GENERATE A FULL TETRAMERIC MOLECULE WHEN APPLIED TO THE MONOMER PRESENTED IN THIS ENTRY. THE MONOMER PRESENTED IN THIS ENTRY IS THE *RED* SUBUNIT. *MTRIX 1* ROTATES THE *RED* SUBUNIT ABOUT THE P AXIS TO GENERATE THE *BLUE* SUBUNIT. *MTRIX 2* ROTATES THE *RED* SUBUNIT ABOUT THE Q AXIS TO GENERATE THE *YELLOW* SUBUNIT. *MTRIX 3* ROTATES THE *RED* SUBUNIT ABOUT THE *R* AXIS TO GENERATES THE *GREEN* SUBUNIT. THE TETRAMERIC ENZYME CRYSTALLIZES IN SPACE GROUP C 2 WITH SIX TETRAMERS IN THE UNIT CELL. THE OVERALL ARRANGEMENT IS CLOSE TO SPACE GROUP P 31 2 1 (WHICH IS A SUPERGROUP OF C 2), AND ALL TETRAMERS HAVE GOOD LOCAL 222 SYMMETRY. THE *CENTRAL* AND *PERIPHERAL* TETRAMERS ARE RELATED BY AN APPROXIMATE NONCRYSTALLOGRAPHIC 3(1) SCREW AXIS. FRACTIONAL COORDINATES FOR THE ASYMMETRIC UNIT OF THE CRYSTAL CAN BE GENERATED BY APPLYING THE FOLLOWING SIX TRANSFORMATIONS TO THE MONOMER PRESENTED IN THIS ENTRY .003360 .004864 0.000000 0.00000 0.000000 0.000000 .011712 0.00000 .004638 -.003051 0.000000 0.00000 -.003360 .004864 0.000000 0.00000 0.000000 0.000000 -.011712 0.00000 -.004638 -.003051 0.000000 0.00000 -.001966 -.002898 .004763 .27144 -.004865 -.008091 -.006931 .14147 .004657 -.003012 .000247 .67215 .001966 .002898 .004763 .27144 .004865 .008091 -.006931 .14147 -.004657 .003012 .000247 .67215 .001966 -.002898 -.004763 .27144 .004865 -.008091 .006931 .14147 -.004657 -.003012 -.000247 .67215 -.001966 .002898 -.004763 .27144 -.004865 .008091 .006931 .14147 .004657 .003012 -.000247 .67215

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Components

#1: Protein L-LACTATE DEHYDROGENASE


Mass: 35479.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / References: UniProt: P00343, L-lactate dehydrogenase
#2: Sugar ChemComp-AFP / 1,6-di-O-phosphono-alpha-D-fructofuranose / ALPHA FRUCTOSE 1,6-DIPHOSPHATE / 1,6-di-O-phosphono-alpha-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, alpha linking / Mass: 340.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
a-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Nonpolymer detailsTHE METAL ION BINDING SITE HAS NOT YET BEEN IDENTIFIED AND, THEREFORE, NO COORDINATES FOR CO2+ ARE ...THE METAL ION BINDING SITE HAS NOT YET BEEN IDENTIFIED AND, THEREFORE, NO COORDINATES FOR CO2+ ARE INCLUDED IN THIS ENTRY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 3→10 Å / Rfactor Rwork: 0.374
Details: THERE ARE THREE ZONES OF LOW (OR NO) DENSITY CONSISTING OF LYS 102 - LEU 110 (ACTIVE SITE LOOP), GLU 211 - VAL 226 (CRYSTAL CONTACTS), AND ILE 334 - GLN 338 (C-TERMINUS). NO COORDINATES ARE ...Details: THERE ARE THREE ZONES OF LOW (OR NO) DENSITY CONSISTING OF LYS 102 - LEU 110 (ACTIVE SITE LOOP), GLU 211 - VAL 226 (CRYSTAL CONTACTS), AND ILE 334 - GLN 338 (C-TERMINUS). NO COORDINATES ARE PRESENT IN THIS ENTRY FOR THE C-TERMINUS.
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 25 0 2479

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