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

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Basic information

Entry
Database: PDB / ID: 2ilu
TitleCrystal structure of lactaldehyde dehydrogenase from E. coli: the binary complex with NADPH
ComponentsAldehyde dehydrogenase A
KeywordsOXIDOREDUCTASE / NADPH-Lactaldehyde dehydrogenase complex
Function / homology
Function and homology information


glycolaldehyde dehydrogenase / glycolaldehyde dehydrogenase (NAD+) activity / lactaldehyde dehydrogenase / succinate-semialdehyde dehydrogenase (NAD+) activity / rhamnose catabolic process / lactaldehyde dehydrogenase (NAD+) activity / gamma-aminobutyric acid 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; 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Lactaldehyde dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsDi Costanzo, L. / Gomez, G. / 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 3, 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 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)53,3104
Polymers52,3731
Non-polymers9383
Water57632
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)213,24016
Polymers209,4904
Non-polymers3,75012
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 area23410 Å2
ΔGint-199 kcal/mol
Surface area59910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)143.566, 143.566, 108.763
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: -x, -y, z (4); y, x, -z+1/3 (7); -y, -x, -z+1/3 (10)

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Components

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


Mass: 52372.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aldA / Production host: Escherichia coli (E. coli)
References: UniProt: P25553, lactaldehyde dehydrogenase, glycolaldehyde dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris or Tris, 2.0 M ammonium sulfate, pH pH 6.8 - 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: 2.7→50 Å / Num. obs: 16757 / Redundancy: 14.4 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 22.6

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2HG2

2hg2


Resolution: 2.7→50 Å
RfactorNum. reflectionSelection details
Rfree0.253 1091 random
Rwork0.212 --
obs-15617 -
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 58 32 3756
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.97
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree: 0.2945 / Rfactor Rwork: 0.2506

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