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- PDB-5j78: Crystal structure of an Acetylating Aldehyde Dehydrogenase from G... -

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Basic information

Entry
Database: PDB / ID: 5j78
TitleCrystal structure of an Acetylating Aldehyde Dehydrogenase from Geobacillus thermoglucosidasius
ComponentsAcetaldehyde dehydrogenase (Acetylating)
KeywordsOXIDOREDUCTASE / Acetylating aldehyde dehydrogenase
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
ACETATE ION / Acetaldehyde dehydrogenase (Acetylating)
Similarity search - Component
Biological speciesGeobacillus thermoglucosidasius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 ...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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
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)212,87651
Polymers209,0844
Non-polymers3,79347
Water22,8611269
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26520 Å2
ΔGint-86 kcal/mol
Surface area60180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.579, 109.120, 196.243
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: 52270.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The strain used is from Geobacillus thermoglucosidasius NCIMB 11955
Source: (gene. exp.) Geobacillus thermoglucosidasius (bacteria)
Strain: NCIMB 11955 / Gene: AcAldDH / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0M1QQ83, acetaldehyde dehydrogenase (acetylating)
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1269 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M sodium acetate pH 4.8, 0.2M MgCl2, 15% (v/v) PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 123787 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 15.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.23 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K9D

3k9d


Resolution: 2.1→49.289 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.18
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 6236 5.04 %random selection
Rwork0.1431 ---
obs0.1459 123659 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13597 0 246 1269 15112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114419
X-RAY DIFFRACTIONf_angle_d1.14219456
X-RAY DIFFRACTIONf_dihedral_angle_d14.5315423
X-RAY DIFFRACTIONf_chiral_restr0.0472272
X-RAY DIFFRACTIONf_plane_restr0.0052521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.1240.27191480.21723779X-RAY DIFFRACTION97
2.124-2.1490.27042200.20473882X-RAY DIFFRACTION100
2.149-2.17520.24671970.19163850X-RAY DIFFRACTION100
2.1752-2.20270.29122050.1893875X-RAY DIFFRACTION100
2.2027-2.23170.23882140.17243885X-RAY DIFFRACTION100
2.2317-2.26230.22482060.16813885X-RAY DIFFRACTION100
2.2623-2.29460.21231910.16053902X-RAY DIFFRACTION100
2.2946-2.32880.23812230.15823852X-RAY DIFFRACTION100
2.3288-2.36520.22412010.15533894X-RAY DIFFRACTION100
2.3652-2.4040.23352020.15413891X-RAY DIFFRACTION100
2.404-2.44540.22942090.15553875X-RAY DIFFRACTION100
2.4454-2.48990.22551800.1433914X-RAY DIFFRACTION100
2.4899-2.53780.22492230.14113883X-RAY DIFFRACTION100
2.5378-2.58960.2032000.13793897X-RAY DIFFRACTION100
2.5896-2.64590.19582110.14123891X-RAY DIFFRACTION100
2.6459-2.70740.22062290.14083856X-RAY DIFFRACTION100
2.7074-2.77520.21332090.14123911X-RAY DIFFRACTION100
2.7752-2.85020.19452050.14033921X-RAY DIFFRACTION100
2.8502-2.9340.1961940.14063908X-RAY DIFFRACTION100
2.934-3.02870.23132020.14763940X-RAY DIFFRACTION100
3.0287-3.1370.18492140.143889X-RAY DIFFRACTION100
3.137-3.26250.20291920.13143959X-RAY DIFFRACTION100
3.2625-3.4110.17762130.13163939X-RAY DIFFRACTION100
3.411-3.59080.1692210.13713891X-RAY DIFFRACTION100
3.5908-3.81570.17892030.1323968X-RAY DIFFRACTION100
3.8157-4.11010.17152390.12563924X-RAY DIFFRACTION100
4.1101-4.52350.16622390.11253942X-RAY DIFFRACTION100
4.5235-5.17740.15362120.11454003X-RAY DIFFRACTION100
5.1774-6.52070.18362300.15134019X-RAY DIFFRACTION100
6.5207-49.30310.17082040.15924198X-RAY DIFFRACTION99

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