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- PDB-2imp: Crystal structure of lactaldehyde dehydrogenase from E. coli: the... -

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Basic information

Entry
Database: PDB / ID: 2imp
TitleCrystal structure of lactaldehyde dehydrogenase from E. coli: the ternary complex with lactate (occupancy 0.5) and NADH. Crystals soaked with (L)-Lactate.
ComponentsLactaldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / protein-lactate-NADH ternary complex
Function / homology
Function and homology information


glycolaldehyde dehydrogenase / glycolaldehyde dehydrogenase activity / lactaldehyde dehydrogenase / lactaldehyde dehydrogenase activity / succinate-semialdehyde dehydrogenase (NAD+) activity / gamma-aminobutyric acid catabolic process / rhamnose catabolic process / L-fucose catabolic process / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LACTIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Lactaldehyde dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsDi Costanzo, L. / Gomez, G.A. / Christianson, D.W.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of Lactaldehyde Dehydrogenase from Escherichia coli and Inferences Regarding Substrate and Cofactor Specificity.
Authors: Di Costanzo, L. / Gomez, G.A. / Christianson, D.W.
History
DepositionOct 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Mar 27, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Experimental preparation / Structure summary
Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / struct / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.pdbx_pH_range / _exptl_crystal_grow.temp / _struct.title / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3205
Polymers52,3731
Non-polymers9484
Water3,981221
1
A: Lactaldehyde dehydrogenase
hetero molecules

A: Lactaldehyde dehydrogenase
hetero molecules

A: Lactaldehyde dehydrogenase
hetero molecules

A: Lactaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,28120
Polymers209,4904
Non-polymers3,79116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area23160 Å2
ΔGint-199 kcal/mol
Surface area60020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)143.034, 143.034, 109.364
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Detailstetramer generated by the application of the following operations symmetry to the monomer: 1) x,y,z 4)-x,-y,z 7) y,x,-z+1/3 10) -y,-x,-z+1/3

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Components

#1: Protein Lactaldehyde dehydrogenase / / Aldehyde dehydrogenase A / Glycolaldehyde dehydrogenase


Mass: 52372.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P25553, glycolaldehyde dehydrogenase, lactaldehyde dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical ChemComp-LAC / LACTIC ACID / Lactic acid


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 2.0 M Ammoniun sulfate, 0.1 M Bis-tris or Tris, pH 6.8 - 7.4, crystals were soaked with lactate; VAPOR DIFFUSION, HANGING DROP
PH range: 6.8 - 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 36157 / Redundancy: 8 % / Rmerge(I) obs: 0.122
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.542 / Num. unique all: 3511

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Processing

Software
NameClassification
DNAdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→50 Å
RfactorNum. reflection
Rfree0.234 2412
Rwork0.2 -
all-36157
obs-34320
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 60 221 3947
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree: 0.2753 / Rfactor Rwork: 0.246

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