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- PDB-2hg2: Structure of Lactaldehyde Dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 2hg2
TitleStructure of Lactaldehyde Dehydrogenase
ComponentsAldehyde dehydrogenase A
KeywordsOXIDOREDUCTASE / dehydrogenase / NAD dependent
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
Lactaldehyde dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 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
DepositionJun 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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: Aldehyde dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5173
Polymers52,3251
Non-polymers1922
Water1,964109
1
A: Aldehyde dehydrogenase A
hetero molecules

A: Aldehyde dehydrogenase A
hetero molecules

A: Aldehyde dehydrogenase A
hetero molecules

A: Aldehyde dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,06712
Polymers209,2984
Non-polymers7698
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 area19180 Å2
ΔGint-177 kcal/mol
Surface area61100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)143.940, 143.940, 108.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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


Mass: 52324.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aldA, ald / Production host: Escherichia coli (E. coli)
References: UniProt: P25553, lactaldehyde dehydrogenase, glycolaldehyde dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.11 Å3/Da / Density % sol: 60.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: bis-tris pH 6.5, 2.0 M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1831 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2005 / Details: KOHZU: Double crystal Si(111)
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1831 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 34109 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.118

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.2→50 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 1595 random
Rwork0.221 --
all-32461 -
obs-32461 -
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3663 0 10 109 3782
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005843
X-RAY DIFFRACTIONc_angle_deg1.25763
X-RAY DIFFRACTIONc_dihedral_angle_d22.71
X-RAY DIFFRACTIONc_improper_angle_d0.85

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