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- PDB-5eeb: Apo form of thermostable aldehyde dehydrogenase from Pyrobaculum ... -

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Basic information

Entry
Database: PDB / ID: 5eeb
TitleApo form of thermostable aldehyde dehydrogenase from Pyrobaculum sp. 1860
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Thermostable aldehyde dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide binding
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 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
Aldehyde dehydrogenase
Similarity search - Component
Biological speciesPyrobaculum ferrireducens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.038 Å
AuthorsPetrova, T.E. / Bezsudnova, E.Y. / Boyko, K.M. / Mardanov, A.V. / Gumerov, V.M. / Ravin, N.V. / Popov, V.O.
CitationJournal: Archaea / Year: 2016
Title: NADP-Dependent Aldehyde Dehydrogenase from ArchaeonPyrobaculum sp.1860: Structural and Functional Features.
Authors: Bezsudnova, E.Y. / Petrova, T.E. / Artemova, N.V. / Boyko, K.M. / Shabalin, I.G. / Rakitina, T.V. / Polyakov, K.M. / Popov, V.O.
History
DepositionOct 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)435,6748
Polymers435,6748
Non-polymers00
Water00
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)217,8374
Polymers217,8374
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22240 Å2
ΔGint-80 kcal/mol
Surface area59960 Å2
MethodPISA
2
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)217,8374
Polymers217,8374
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22230 Å2
ΔGint-89 kcal/mol
Surface area60090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.240, 207.230, 164.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Aldehyde dehydrogenase


Mass: 54459.207 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum ferrireducens (archaea) / Gene: P186_1147 / Production host: Escherichia coli (E. coli) / Strain (production host): Dlt1270/prare2 / References: UniProt: G7VCG0

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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: 3.61 Å3/Da / Density % sol: 65.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50 mM HEPES, NaCl, beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.984 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.038→29.771 Å / Num. obs: 120589 / % possible obs: 98.94 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.266 / Net I/σ(I): 7.71
Reflection shellResolution: 3.038→3.2 Å / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.26

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H73

4h73


Resolution: 3.038→29.771 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 6053 5.02 %Random selection
Rwork0.202 ---
obs0.2048 120493 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.038→29.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30043 0 0 0 30043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0130675
X-RAY DIFFRACTIONf_angle_d1.27441597
X-RAY DIFFRACTIONf_dihedral_angle_d14.84411167
X-RAY DIFFRACTIONf_chiral_restr0.0514702
X-RAY DIFFRACTIONf_plane_restr0.0075380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0383-3.07280.39351760.31923259X-RAY DIFFRACTION85
3.0728-3.10890.40281900.31923775X-RAY DIFFRACTION99
3.1089-3.14680.35532130.30393759X-RAY DIFFRACTION99
3.1468-3.18650.36872050.31293817X-RAY DIFFRACTION99
3.1865-3.22840.37852320.29533785X-RAY DIFFRACTION99
3.2284-3.27260.34812130.29573720X-RAY DIFFRACTION100
3.2726-3.31930.33911890.27263835X-RAY DIFFRACTION100
3.3193-3.36880.32932210.25633785X-RAY DIFFRACTION100
3.3688-3.42130.34471690.24483847X-RAY DIFFRACTION99
3.4213-3.47730.31312040.24513801X-RAY DIFFRACTION100
3.4773-3.53720.31672080.24863792X-RAY DIFFRACTION99
3.5372-3.60140.28661880.2463835X-RAY DIFFRACTION99
3.6014-3.67060.29222170.22993784X-RAY DIFFRACTION99
3.6706-3.74540.27061980.22653842X-RAY DIFFRACTION100
3.7454-3.82660.26681890.20273799X-RAY DIFFRACTION100
3.8266-3.91550.23641880.19023867X-RAY DIFFRACTION100
3.9155-4.01320.26531870.18933828X-RAY DIFFRACTION100
4.0132-4.12140.24382100.17983795X-RAY DIFFRACTION99
4.1214-4.24230.2342040.17953800X-RAY DIFFRACTION99
4.2423-4.37890.22631920.16933823X-RAY DIFFRACTION99
4.3789-4.53480.18872110.15813840X-RAY DIFFRACTION100
4.5348-4.71570.20431840.14623868X-RAY DIFFRACTION100
4.7157-4.92940.17391940.14613857X-RAY DIFFRACTION100
4.9294-5.1880.21211860.16273889X-RAY DIFFRACTION100
5.188-5.51120.23931880.16013873X-RAY DIFFRACTION100
5.5112-5.93360.222050.17163859X-RAY DIFFRACTION100
5.9336-6.5250.2292130.1763891X-RAY DIFFRACTION100
6.525-7.45620.20452070.15433897X-RAY DIFFRACTION99
7.4562-9.34560.15732330.12913906X-RAY DIFFRACTION99
9.3456-29.77210.20342390.18654012X-RAY DIFFRACTION98

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