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- PDB-5euy: Thermostable aldehyde dehydrogenase from Pyrobaculum sp.1860 comp... -

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Basic information

Entry
Database: PDB / ID: 5euy
TitleThermostable aldehyde dehydrogenase from Pyrobaculum sp.1860 complexed with NADP+
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Aldehyde dehydrogenase / thermostable
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesPyrobaculum sp. 1860 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.06 Å
AuthorsPetrova, T. / Bezsudnova, E.Y. / Boyko, K.M. / Nikolaeva, A.Y. / Rakitina, T.V. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RFBR Russian Federation
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
DepositionNov 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,62116
Polymers435,6748
Non-polymers5,9478
Water52,2442900
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,8108
Polymers217,8374
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26170 Å2
ΔGint-111 kcal/mol
Surface area59680 Å2
MethodPISA
2
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,8108
Polymers217,8374
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26150 Å2
ΔGint-105 kcal/mol
Surface area59550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.770, 208.050, 165.400
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 sp. 1860 (archaea) / Gene: P186_1147 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): Dlt1270/prare2 / References: UniProt: G7VCG0
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2900 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Imidazole ph 6.5, 1.0 M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.06→59.057 Å / Num. obs: 387726 / % possible obs: 99.34 % / Observed criterion σ(I): 8.3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.3
Reflection shellResolution: 2.06→2.12 Å / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementStarting model: 4H73

4h73


Resolution: 2.06→59.057 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 1999 0.52 %Random selection
Rwork0.1957 ---
obs0.1959 387726 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→59.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30116 0 312 2900 33328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831457
X-RAY DIFFRACTIONf_angle_d1.05842779
X-RAY DIFFRACTIONf_dihedral_angle_d14.93111572
X-RAY DIFFRACTIONf_chiral_restr0.0434825
X-RAY DIFFRACTIONf_plane_restr0.0055475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.11160.34141410.312127315X-RAY DIFFRACTION99
2.1116-2.16860.26991430.283527470X-RAY DIFFRACTION100
2.1686-2.23250.29691430.261827607X-RAY DIFFRACTION100
2.2325-2.30450.32341420.254127390X-RAY DIFFRACTION100
2.3045-2.38690.28671420.24127527X-RAY DIFFRACTION100
2.3869-2.48250.2851430.237627483X-RAY DIFFRACTION100
2.4825-2.59540.28491420.228327443X-RAY DIFFRACTION99
2.5954-2.73230.28061430.2227537X-RAY DIFFRACTION100
2.7323-2.90350.25761420.21427515X-RAY DIFFRACTION99
2.9035-3.12760.24481430.206427550X-RAY DIFFRACTION99
3.1276-3.44230.22541430.194327459X-RAY DIFFRACTION99
3.4423-3.94040.22191430.169127676X-RAY DIFFRACTION99
3.9404-4.96410.16911410.144227443X-RAY DIFFRACTION98
4.9641-59.08080.19011480.166628312X-RAY DIFFRACTION99

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