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- PDB-9ldb: DESIGN AND SYNTHESIS OF NEW ENZYMES BASED ON THE LACTATE DEHYDROG... -

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Entry
Database: PDB / ID: 9ldb
TitleDESIGN AND SYNTHESIS OF NEW ENZYMES BASED ON THE LACTATE DEHYDROGENASE FRAMEWORK
ComponentsLACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE(CHOH(D)-NAD+(A))
Function / homology
Function and homology information


Pyruvate metabolism / L-lactate dehydrogenase / L-lactate dehydrogenase activity / carboxylic acid metabolic process / cytoplasm
Similarity search - Function
L-lactate dehydrogenase active site. / L-lactate dehydrogenase / 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 active site. / L-lactate dehydrogenase / 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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsDunn, C.R. / Holbrook, J.J. / Muirhead, H.
CitationJournal: Philos.Trans.R.Soc.London,Ser.B / Year: 1991
Title: Design and synthesis of new enzymes based on the lactate dehydrogenase framework.
Authors: Dunn, C.R. / Wilks, H.M. / Halsall, D.J. / Atkinson, T. / Clarke, A.R. / Muirhead, H. / Holbrook, J.J.
History
DepositionNov 26, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
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][3] / _atom_sites.fract_transf_vector[3] / _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[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_rmsd_angle.PDB_ins_code_1 / _pdbx_validate_rmsd_angle.PDB_ins_code_2 / _pdbx_validate_rmsd_angle.PDB_ins_code_3 / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_angle.linker_flag / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.vector[3] / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Remark 700SHEET AFTER ROTATION OF THE A AND B SUBUNITS ABOUT THE CRYSTALLOGRAPHIC X AXIS, THE GENERATED C AND ...SHEET AFTER ROTATION OF THE A AND B SUBUNITS ABOUT THE CRYSTALLOGRAPHIC X AXIS, THE GENERATED C AND D SUBUNITS FORM EXTENSIONS TO SHEET 3 IN THE SHEET RECORDS BELOW. THE SYMMETRY-GENERATED SHEET RECORDS ARE PRESENTED AS A REMARK BECAUSE PDB SPECIFICATIONS DO NOT ALLOW THE INCLUSION OF STRANDS WHOSE COORDINATES ARE NOT PRESENTED IN THE ENTRY: EXTENSION TO SHEET 3 OF A SUBUNIT 3A 4 HIS D 9 LEU D 11 -1 N HIS D 9 O VAL A 302 EXTENSION TO SHEET 3 OF B SUBUNIT 3B 4 HIS C 9 LEU C 11 -1 N HIS C 9 O VAL B 302 STRAND 2 OF SHEETS 2A AND 2B IS BIFURCATED. EACH OF THESE IS REPRESENTED BY TWO SHEETS, 2AA AND 2BA AND 2AB AND 2BB BELOW, WHERE THE FIRST STRAND OF 2AA IS IDENTICAL TO THE FIRST STRAND OF 2BA AND THE FIRST STRAND OF 2AB IS IDENTICAL TO THE FIRST STRAND OF 2BB.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,8298
Polymers73,1252
Non-polymers1,7046
Water2,720151
1
A: LACTATE DEHYDROGENASE
B: LACTATE DEHYDROGENASE
hetero molecules

A: LACTATE DEHYDROGENASE
B: LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,65816
Polymers146,2504
Non-polymers3,40812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area29110 Å2
ΔGint-282 kcal/mol
Surface area41230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.300, 136.390, 86.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: RESIDUES PRO A 141 AND PRO B 141 ARE CIS PROLINES.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (-0.892463, 0.451425), (0.450814, 0.892463), (-1) / Vector: 14)
DetailsTWO LDH SUBUNITS ARE INCLUDED. THE A-SUBUNIT HAS NADH AND SULPHATE IN THE ACTIVE SITE. THE B-SUBUNIT HAS NADH AND OXAMATE IN THE ACTIVE SITE. BOTH SUBUNITS HAVE SULPHATE BOUND AT A REMOTE SITE. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. THE *SCALE* TRANSFORMATION BELOW GENERATES FRACTIONAL COORDINATES WITH RESPECT TO SPACE GROUP P 21 21 2.

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Components

#1: Protein LACTATE DEHYDROGENASE /


Mass: 36562.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00339, L-lactate dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-OXM / OXAMIC ACID / Oxamic acid


Mass: 89.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES ARE NUMBERED ACCORDING TO THE STANDARD LDH NUMBERING SYSTEM DESCRIBED BY S.S.TAYLOR ET AL. ...RESIDUES ARE NUMBERED ACCORDING TO THE STANDARD LDH NUMBERING SYSTEM DESCRIBED BY S.S.TAYLOR ET AL., IN PROC.NAT.ACAD.SCI.USA V.70 1790 1973.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.15 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→20 Å / σ(F): 0 /
RfactorNum. reflection
obs0.22 28869
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5136 0 109 151 5396
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.060.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0630.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.4681
X-RAY DIFFRACTIONp_mcangle_it0.8651.5
X-RAY DIFFRACTIONp_scbond_it0.5841
X-RAY DIFFRACTIONp_scangle_it0.9111.5
X-RAY DIFFRACTIONp_plane_restr0.0220.02
X-RAY DIFFRACTIONp_chiral_restr0.1540.15
X-RAY DIFFRACTIONp_singtor_nbd0.1950.5
X-RAY DIFFRACTIONp_multtor_nbd0.2830.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2260.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.13
X-RAY DIFFRACTIONp_staggered_tor24.315
X-RAY DIFFRACTIONp_orthonormal_tor33.230
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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