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- PDB-2ldb: STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPH... -

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Entry
Database: PDB / ID: 2ldb
TitleSTRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE
ComponentsL-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE(CHOH(D)-NAD(A))
Function / homology
Function and homology information


L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / glycolytic process / NAD binding / 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-beta-D-fructofuranose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-lactate dehydrogenase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsPiontek, K. / Rossmann, M.G.
Citation
Journal: Proteins / Year: 1990
Title: Structure determination and refinement of Bacillus stearothermophilus lactate dehydrogenase.
Authors: Piontek, K. / Chakrabarti, P. / Schar, H.P. / Rossmann, M.G. / Zuber, H.
#1: Journal: Hoppe-Seyler's Z.Physiol.Chem. / Year: 1987
Title: Nucleotide Sequences of Lactate Dehydrogenase Genes from the Thermophilic Bacteria Bacillus Stearothermophilus, B. Caldolyticus and B. Caldotenax
Authors: Zuelli, F. / Weber, H. / Zuber, H.
#2: Journal: J.Mol.Biol. / Year: 1982
Title: Crystallization of Lactate Dehydrogenase from Bacillus Stearothermophilus
Authors: Schaer, H.-P. / Zuber, H. / Rossmann, M.G.
History
DepositionMar 27, 1989Processing site: BNL
Revision 1.0Jul 12, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / 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_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / 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][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] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _chem_comp.pdbx_synonyms / _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] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_planes.rmsd / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _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_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3]
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-LACTATE DEHYDROGENASE
B: L-LACTATE DEHYDROGENASE
C: L-LACTATE DEHYDROGENASE
D: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,71318
Polymers139,6114
Non-polymers4,10214
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.800, 86.800, 356.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Atom site foot note1: RESIDUE PRO 139 IS A CIS PROLINE.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.03171856, 0.99562093, -0.08905187), (0.99540212, 0.02350737, -0.09154613), (-0.08928224, -0.09180314, -0.9917888)-10.06015, 42.021, 360.41834
2given(-0.99751173, -0.00875464, -0.07061917), (-0.00861964, -0.96967303, 0.24463198), (-0.06931404, 0.24387146, 0.96718475)44.2731, 39.82597, -3.37725
3given(0.02923029, -0.98686628, 0.15967104), (-0.98678248, -0.05383434, -0.15308584), (0.15859629, -0.15206833, -0.97539595)28.48789, 87.33591, 356.15891
DetailsNON-CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS CORRESPONDING TO THE THREE ORTHOGONAL MOLECULAR TWO-FOLD SYMMETRY AXES ARE PRESENTED ON THE *MTRIX* RECORDS BELOW.

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Components

#1: Protein
L-LACTATE DEHYDROGENASE


Mass: 34902.723 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
References: UniProt: P00344, L-lactate dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Sugar ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUES IN THIS ENTRY ARE NUMBERED SEQUENTIALLY FROM 15 - 331. SEE C. ABAD-ZAPATERO, J. P. ...THE RESIDUES IN THIS ENTRY ARE NUMBERED SEQUENTIALLY FROM 15 - 331. SEE C. ABAD-ZAPATERO, J. P. GRIFFITH, J. L. SUSSMAN, M. G. ROSSMANN, J.MOL.BIOL., V. 198, P. 445 (1987) FOR AN EXPLANATION OF THE NUMBERING SYSTEM USED IN 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growDetails: THE ENZYME WAS COCRYSTALLIZED IN THE PRESENCE OF THE COENZYME NAD AND THE ACTIVATOR FBP. THE NAD MOLECULE IS SITUATED AT THE LDH COENZYME BINDING SITE. ONE FBP MOLECULE BINDS ACROSS THE P- ...Details: THE ENZYME WAS COCRYSTALLIZED IN THE PRESENCE OF THE COENZYME NAD AND THE ACTIVATOR FBP. THE NAD MOLECULE IS SITUATED AT THE LDH COENZYME BINDING SITE. ONE FBP MOLECULE BINDS ACROSS THE P-AXIS. THE P-AXIS INTERSECTS THE ACTIVATOR MOLECULE GIVING RISE TO A STATISTICAL DISORDER (OCCUPANCY 0.5) AS FBP HAS ONLY PSEUDO-TWO-FOLD SYMMETRY. ONE SULFATE (SO4 3) BINDS AT THE SUBSTRATE BINDING SITE. ANOTHER SULFATE (SO4 4) IS CLOSE TO THE R-AXIS INTERFACE.
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion
Details: taken from Schar, H-P. et al (1982). J. Mol. Biol., 154, 349-353.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
136 %satammonium sulfate11
250 mMPIPES11
320 mMNADH11
420 mMFDP11

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Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 50 Å / Num. obs: 24793 / % possible obs: 79.8 % / Observed criterion σ(I): 2 / Num. measured all: 76407 / Rmerge(I) obs: 0.109

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 3→6 Å / Rfactor obs: 0.26
Details: THE ASSIGNMENT OF DONOR AND ACCEPTOR WAS ARBITRARY FOR THE FOLLOWING HYDROGEN BONDS NO7 NAD 1 O3 SO4 3 O3 SO4 3 OD1 ASP 46 O4 SO4 4 O LYS 74 O3 SO4 4 O ALA 45 O3 SO4 4 O GLY 43
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9344 0 256 50 9650
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0430.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.961.5
X-RAY DIFFRACTIONp_mcangle_it1.722
X-RAY DIFFRACTIONp_scbond_it1.362
X-RAY DIFFRACTIONp_scangle_it2.323
X-RAY DIFFRACTIONp_plane_restr0.0230.03
X-RAY DIFFRACTIONp_chiral_restr0.1660.17
X-RAY DIFFRACTIONp_singtor_nbd0.2490.5
X-RAY DIFFRACTIONp_multtor_nbd0.3040.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2540.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.84
X-RAY DIFFRACTIONp_staggered_tor20.215
X-RAY DIFFRACTIONp_orthonormal_tor31.120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 21007 / Rfactor obs: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS

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