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- PDB-5j7i: Crystal structure of a Geobacillus thermoglucosidasius Acetylatin... -

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Basic information

Entry
Database: PDB / ID: 5j7i
TitleCrystal structure of a Geobacillus thermoglucosidasius Acetylating Aldehyde Dehydrogenase in complex with ADP
ComponentsAcetaldehyde dehydrogenase (Acetylating)
KeywordsOXIDOREDUCTASE / Acetylating aldehyde dehydrogenase / complex
Function / homology
Function and homology information


acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / nucleotide binding
Similarity search - Function
Acetaldehyde dehydrogenase, acetylating / 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase ...Acetaldehyde dehydrogenase, acetylating / 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 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5-DIPHOSPHORIBOSE / Acetaldehyde dehydrogenase (Acetylating)
Similarity search - Component
Biological speciesGeobacillus thermoglucosidasius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsCrennell, S.J. / Extance, J.P. / Danson, M.J.
CitationJournal: Protein Sci. / Year: 2016
Title: Structure of an acetylating aldehyde dehydrogenase from the thermophilic ethanologen Geobacillus thermoglucosidasius.
Authors: Extance, J. / Danson, M.J. / Crennell, S.J.
History
DepositionApr 6, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetaldehyde dehydrogenase (Acetylating)
B: Acetaldehyde dehydrogenase (Acetylating)
C: Acetaldehyde dehydrogenase (Acetylating)
D: Acetaldehyde dehydrogenase (Acetylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,9658
Polymers209,1244
Non-polymers1,8414
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16120 Å2
ΔGint-56 kcal/mol
Surface area64940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.054, 109.543, 204.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Acetaldehyde dehydrogenase (Acetylating)


Mass: 52280.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermoglucosidasius (strain C56-YS93) (bacteria)
Strain: C56-YS93 / Gene: Geoth_3234 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0M1QQ83, acetaldehyde dehydrogenase (acetylating)
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.94 % / Description: thin and plate-like
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: protein solution containing 10.7mg/ml protein, 0.5mM acetyl-CoA and 5mM NAD+ was mixed 1:1 with 0.1M MMT buffer pH5.0, 21 to 23% PEG 1500

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 14328 / % possible obs: 78 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.267 / Net I/σ(I): 3.87
Reflection shellResolution: 4→4.07 Å / Redundancy: 2.26 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.26 / % possible all: 70.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J78

5j78


Resolution: 4→42.668 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2825 717 5.03 %random
Rwork0.2295 ---
obs0.2322 14256 78.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4→42.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13652 0 117 0 13769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613972
X-RAY DIFFRACTIONf_angle_d1.23518932
X-RAY DIFFRACTIONf_dihedral_angle_d14.325205
X-RAY DIFFRACTIONf_chiral_restr0.052255
X-RAY DIFFRACTIONf_plane_restr0.0052427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0031-4.31190.31141300.23392478X-RAY DIFFRACTION73
4.3119-4.74530.28041540.24682541X-RAY DIFFRACTION75
4.7453-5.43080.29221580.26022654X-RAY DIFFRACTION78
5.4308-6.83770.35311340.29782820X-RAY DIFFRACTION81
6.8377-42.67010.21161410.15263046X-RAY DIFFRACTION84

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