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- PDB-5f2c: Thermostable aldehyde dehydrogenase from Pyrobaculum sp. 1860 cry... -

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Basic information

Entry
Database: PDB / ID: 5f2c
TitleThermostable aldehyde dehydrogenase from Pyrobaculum sp. 1860 crystallized in microgravity (complex with NADP+)
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesPyrobaculum ferrireducens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 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
DepositionDec 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 14, 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
SupersessionOct 29, 2025ID: 4NMK
Revision 1.3Oct 29, 2025Group: Advisory / Structure summary / Category: pdbx_database_PDB_obs_spr / pdbx_entry_details

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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)441,71317
Polymers435,6748
Non-polymers6,0399
Water57,3603184
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,9039
Polymers217,8374
Non-polymers3,0665
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26370 Å2
ΔGint-112 kcal/mol
Surface area60360 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 area26140 Å2
ΔGint-114 kcal/mol
Surface area60050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.356, 208.296, 163.811
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
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3184 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.63 Å3/Da / Density % sol: 66.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystallization details 50 mM HEPES pH 7.5; 50 mM NaCl; 100 mM Imidazole pH 6.5; 1.6M Sodium acetate trihydrate. The crystal was grown in a microgravity environment.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.898→29.145 Å / Num. all: 4133317 / Num. obs: 493450 / % possible obs: 87.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 23
Reflection shellResolution: 1.898→1.9193 Å / % possible all: 22

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H73

4h73


Resolution: 1.898→29.145 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 21753 5.01 %Random selection
Rwork0.1836 ---
obs0.1854 433908 87.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.898→29.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30163 0 318 3184 33665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831811
X-RAY DIFFRACTIONf_angle_d1.02343292
X-RAY DIFFRACTIONf_dihedral_angle_d14.43611790
X-RAY DIFFRACTIONf_chiral_restr0.0424888
X-RAY DIFFRACTIONf_plane_restr0.0055548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8978-1.91930.26591710.24183499X-RAY DIFFRACTION22
1.9193-1.94190.29033090.24765941X-RAY DIFFRACTION38
1.9419-1.96560.27883750.24536935X-RAY DIFFRACTION44
1.9656-1.99050.27044010.23087934X-RAY DIFFRACTION51
1.9905-2.01660.2845060.22479208X-RAY DIFFRACTION59
2.0166-2.04430.28865720.232310727X-RAY DIFFRACTION69
2.0443-2.07350.26366260.229712335X-RAY DIFFRACTION79
2.0735-2.10440.24726950.222513512X-RAY DIFFRACTION87
2.1044-2.13730.26657290.22714343X-RAY DIFFRACTION92
2.1373-2.17230.25188500.225414818X-RAY DIFFRACTION95
2.1723-2.20980.2527920.225115279X-RAY DIFFRACTION98
2.2098-2.24990.24518190.216315395X-RAY DIFFRACTION99
2.2499-2.29320.2698010.214415543X-RAY DIFFRACTION99
2.2932-2.340.25998160.214915589X-RAY DIFFRACTION100
2.34-2.39080.24888200.211115521X-RAY DIFFRACTION100
2.3908-2.44640.25848290.211915680X-RAY DIFFRACTION100
2.4464-2.50760.25417750.208115671X-RAY DIFFRACTION100
2.5076-2.57530.26138380.200415644X-RAY DIFFRACTION100
2.5753-2.6510.22928160.195615636X-RAY DIFFRACTION100
2.651-2.73660.23598570.193315622X-RAY DIFFRACTION100
2.7366-2.83430.22798540.194115631X-RAY DIFFRACTION100
2.8343-2.94770.22498320.193415651X-RAY DIFFRACTION100
2.9477-3.08170.24248310.197615700X-RAY DIFFRACTION100
3.0817-3.24390.23038230.191215680X-RAY DIFFRACTION100
3.2439-3.44690.19788180.17515682X-RAY DIFFRACTION100
3.4469-3.71250.20878590.168315689X-RAY DIFFRACTION100
3.7125-4.08520.17857900.151815781X-RAY DIFFRACTION99
4.0852-4.67430.16588380.135215760X-RAY DIFFRACTION99
4.6743-5.88120.17668480.145115856X-RAY DIFFRACTION99
5.8812-29.14810.17868630.16615893X-RAY DIFFRACTION97

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