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- PDB-1hyh: CRYSTAL STRUCTURE OF L-2-HYDROXYISOCAPROATE DEHYDROGENASE FROM LA... -

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Entry
Database: PDB / ID: 1hyh
TitleCRYSTAL STRUCTURE OF L-2-HYDROXYISOCAPROATE DEHYDROGENASE FROM LACTOBACILLUS CONFUSUS AT 2.2 ANGSTROMS RESOLUTION-AN EXAMPLE OF STRONG ASYMMETRY BETWEEN SUBUNITS
ComponentsL-2-HYDROXYISOCAPROATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE (CHOH(D)-NAD+(A)) / L-2-HYDROXYCARBOXYLATE DEHYDROGENASE / L-LACTATE DEHYDROGENASE
Function / homology
Function and homology information


carboxylic acid metabolic process / L-lactate dehydrogenase activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / carbohydrate metabolic process
Similarity search - Function
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 ...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 / L-2-hydroxyisocaproate dehydrogenase
Similarity search - Component
Biological speciesWeissella confusa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsNiefind, K. / Hecht, H.-J. / Schomburg, D.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of L-2-hydroxyisocaproate dehydrogenase from Lactobacillus confusus at 2.2 A resolution. An example of strong asymmetry between subunits.
Authors: Niefind, K. / Hecht, H.J. / Schomburg, D.
#1: Journal: Eur.J.Biochem. / Year: 1994
Title: Deletion Variants of L-Hydroxyisocaproate Dehydrogenase-Probing Substrate Specificity
Authors: Feil, I.K. / Lerch, H.-P. / Schomburg, D.
#2: Journal: Thesis, Technische Universitat Carolo-Wilhelmina Zu Braunschweig
Year: 1993
Title: Roentgenkristallographische Untersuchungen an Drei Mikrobiellen Enzymen: D-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus Casei, L-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus ...Title: Roentgenkristallographische Untersuchungen an Drei Mikrobiellen Enzymen: D-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus Casei, L-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus Confusus, Alkalische Protease Aus Bacillus Alcalophilus(Slash)Variante Q59R (German, with English Summary)
Authors: Niefind, K.
#3: Journal: Gene / Year: 1989
Title: Cloning, Sequencing and Expression of the L-2-Hydroxyisocaproate Dehydrogenase-Encoding Gene of Lactobacillus Confusus in Escherichia Coli
Authors: Lerch, H.-P. / Frank, R. / Collins, J.
#4: Journal: Appl.Microbiol.Biotechnol. / Year: 1984
Title: L-2-Hydroxyisocaproate Dehydrogenase-A New Enzyme from Lactobacillus Confusus for the Stereospecific Reduction of 2-Ketocarboxylic Acids
Authors: Schuette, H. / Hummel, W. / Kula, M.-R.
History
DepositionJun 5, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: citation / pdbx_database_status ...citation / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _pdbx_database_status.process_site
Revision 2.0Jul 26, 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 / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / 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][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] / _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_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 / _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] / _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
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-2-HYDROXYISOCAPROATE DEHYDROGENASE
B: L-2-HYDROXYISOCAPROATE DEHYDROGENASE
C: L-2-HYDROXYISOCAPROATE DEHYDROGENASE
D: L-2-HYDROXYISOCAPROATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,35812
Polymers132,3214
Non-polymers3,0388
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.900, 135.900, 205.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: CIS PROLINE - PRO A 144 / 2: CIS PROLINE - PRO B 144 / 3: CIS PROLINE - PRO C 144 / 4: CIS PROLINE - PRO D 144
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.4138203, -0.8230033, 0.38903506), (-0.82395423, -0.52036141, -0.22481948), (0.38718299, -0.22729758, -0.89345889)40.51715, 57.1755, -26.3277
2given(-0.5056295, 0.53071066, -0.68031852), (0.52336363, -0.43810263, -0.7310027), (-0.68575975, -0.72539282, -0.05623788)105.33523, -36.71744, 48.21308
3given(-0.90831719, 0.29625052, 0.29517784), (0.29658397, -0.04167296, 0.95437862), (0.29506491, 0.95392095, -0.05001984)133.22056, -21.19756, -20.06121
DetailsNON-CRYSTALLOGRAPHIC SYMMETRY IS WELL PRESERVED AROUND THE MOLECULAR P-AXIS, WHILE IT IS STRONGLY DISTURBED AROUND Q AND R. STRUCTURAL DIFFERENCES BETWEEN THE CHAINS *A* AND *B* ON THE ONE SIDE AND *C* AND *D* ON THE OTHER ARE ESPECIALLY PRONOUNCED IN THE REGION OF THE ACTIVE SITE. MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 21 .. A 331 B 21 .. B 331 0.244 M2 A 21 .. A 331 C 21 .. C 331 5.043 M3 A 21 .. A 331 D 21 .. D 331 5.041 THE FIRST MTRIX-OPERATION DESCRIBES THE TWO-FOLD ROTATION AROUND THE MOLECULAR P-AXIS AND MAPS CHAIN *A* ON CHAIN *B* (INCLUDING THE BOUND NAD+ AND SULFATE, RESPECTIVELY). THE SECOND MTRIX-OPERATION DESCRIBES THE TWO-FOLD ROTATION AROUND THE MOLECULAR Q-AXIS AND MAPS CHAIN *A* ON CHAIN *C* (INCLUDING THE BOUND NAD+ AND SULFATE, RESPECTIVELY). THE THIRD MTRIX-OPERATION DESCRIBES THE TWO-FOLD ROTATION AROUND THE MOLECULAR R-AXIS AND MAPS CHAIN *A* ON CHAIN *D* (INCLUDING THE BOUND NAD+ AND SULFATE, RESPECTIVELY).

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Components

#1: Protein
L-2-HYDROXYISOCAPROATE DEHYDROGENASE / L-HICDH


Mass: 33080.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Weissella confusa (bacteria)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) NUMBER DSM 20196, CELL PLASM
Plasmid: PHL6 / Production host: Escherichia coli (E. coli) / Strain (production host): JM103 / References: UniProt: P14295, L-lactate dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES ARE NUMBERED SEQUENTIALLY STARTING WITH ALA 21 AND ENDING WITH LEU 329. THE REASON FOR ...RESIDUES ARE NUMBERED SEQUENTIALLY STARTING WITH ALA 21 AND ENDING WITH LEU 329. THE REASON FOR BEGINNING WITH 21 IS THAT L-HICDH MISSES AN N-TERMINAL ARM OF ABOUT 20 RESIDUES, WHICH IS PRESENT IN HOMOLOGOUS EUKARYOTIC L-LACTATE DEHYDROGENASES.
Source detailsDSM NUMBER: DSM 20196 (DSM = DEUTSCHE SAMMLUNG VON MIKROORGANISMEN/GERMAN COLLECTION OF MICROORGANISMS)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 70.34 %
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMimidazole HCl1drop
35 mM1dropNaN3
41 mML-dithiothreitol1drop
51.5 Mammonium sulfate1reservoir
650 mMpotassium phosphate1reservoir
71 %(w/w)hexantriole1reservoir
830 mMNAD+1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 30, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.22→15.1 Å / Num. obs: 105688 / % possible obs: 94.9 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Num. obs: 107769 / Rmerge(I) obs: 0.076 / Num. measured all: 388074

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Processing

Software
NameClassification
PROLSQrefinement
MOSFLMdata reduction
RefinementResolution: 2.2→8 Å / σ(F): 2
Details: NO NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS WERE APPLIED IN THE FINAL REFINEMENT. FOUR L-HICDH SUBUNITS ARE INCLUDED. EACH SUBUNIT HAS NAD+ AND A SULFATE ION IN THE ACTIVE SITE. THE *SCALE* ...Details: NO NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS WERE APPLIED IN THE FINAL REFINEMENT. FOUR L-HICDH SUBUNITS ARE INCLUDED. EACH SUBUNIT HAS NAD+ AND A SULFATE ION IN THE ACTIVE SITE. THE *SCALE* TRANSFORMATION BELOW GENERATES FRACTIONAL. COORDINATES WITH RESPECT TO SPACE GROUP P 32 2 1.
RfactorNum. reflection% reflection
Rfree0.25 --
obs0.21 102618 93.2 %
Displacement parametersBiso mean: 27.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8811 0 196 309 9316
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.015
X-RAY DIFFRACTIONp_angle_d0.030.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.261
X-RAY DIFFRACTIONp_mcangle_it1.9641.5
X-RAY DIFFRACTIONp_scbond_it1.3831
X-RAY DIFFRACTIONp_scangle_it1.9531.5
X-RAY DIFFRACTIONp_plane_restr0.0110.015
X-RAY DIFFRACTIONp_chiral_restr0.0650.05
X-RAY DIFFRACTIONp_singtor_nbd0.180.2
X-RAY DIFFRACTIONp_multtor_nbd0.1940.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor22
X-RAY DIFFRACTIONp_staggered_tor1515
X-RAY DIFFRACTIONp_orthonormal_tor33.833.8
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: 'PROLSQ 5.10 IN THE CCP4-SUITE' / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS

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