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- PDB-4nmj: Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexe... -

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Basic information

Entry
Database: PDB / ID: 4nmj
TitleThermostable aldehyde dehydrogenase from Pyrobaculum sp. complexed with NADP+ at 2 A resolution
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / aldehyde oxidation / NADP reduction / intracellular
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 / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsPetrova, T. / Boyko, K.M. / Bezsudnova, E.Y. / Mardanov, A.V. / Gumerov, V.M. / Ravin, N.V. / Popov, V.O.
CitationJournal: To be Published
Title: Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexed with NADP+ at 2 A resolution
Authors: Petrova, T. / Boyko, K.M. / Bezsudnova, E.Y. / Mardanov, A.V. / Gumerov, V.M. / Ravin, N.V. / Popov, V.O.
History
DepositionNov 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
Water55,0183054
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4054
Polymers108,9182
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-43 kcal/mol
Surface area34490 Å2
MethodPISA
2
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4054
Polymers108,9182
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint-43 kcal/mol
Surface area34290 Å2
MethodPISA
3
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4054
Polymers108,9182
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-45 kcal/mol
Surface area34150 Å2
MethodPISA
4
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4054
Polymers108,9182
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-44 kcal/mol
Surface area34080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.479, 184.394, 207.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#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.: 3054 / Source method: isolated from a natural source / Formula: H2O

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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: 3.62 Å3/Da / Density % sol: 65.98 %
Crystal growTemperature: 291 K / Method: gel-tube counter-diffusion / pH: 7.5
Details: 50 mM HEPES, pH 7.5, 50 mM sodium chloride, 100 mM imidazole, pH 6.5, 1.6 M sodium acetate trihydrate, GEL-TUBE COUNTER-DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 7, 2011
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.002→38.09 Å / Num. obs: 418361 / % possible obs: 99.35 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 2.2 / Biso Wilson estimate: 22.82 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 21.7
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.002-2.057198.09
2.057-2.288199.62
2.288-2.545199.53
2.545-2.83199.54
2.83-3.148199.45
3.148-3.501199.26
3.501-3.894199.26
3.894-4.331199.13
4.331-4.817199.28
4.817-5.357199.57
5.357-5.959199.9
5.959-6.6271100
6.627-7.371199.85
7.371-8.198199.83
8.198-9.116199.32
9.118-10.139197.8
10.141-11.278194.56
11.279-12.543192.85
12.544-13.952195.1
13.954-15.507193.19
15.521-17.255198.13
17.274-19.192195.6
19.274-21.348193.75
21.349-23.744190.09
23.782-28.09184.03

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H73

4h73


Resolution: 2.002→28.09 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.86 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 21008 5.02 %RANDOM
Rwork0.2006 ---
all0.21 418781 --
obs0.2022 418361 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.002→28.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30159 0 384 3054 33597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731340
X-RAY DIFFRACTIONf_angle_d1.07442588
X-RAY DIFFRACTIONf_dihedral_angle_d15.32411549
X-RAY DIFFRACTIONf_chiral_restr0.0744795
X-RAY DIFFRACTIONf_plane_restr0.0055464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.002-2.02460.31526660.293912763X-RAY DIFFRACTION96
2.0246-2.04850.31796840.286513159X-RAY DIFFRACTION100
2.0485-2.07340.31457010.277613195X-RAY DIFFRACTION100
2.0734-2.09970.31146880.262413188X-RAY DIFFRACTION100
2.0997-2.12730.30956690.263413213X-RAY DIFFRACTION100
2.1273-2.15640.28937100.256613177X-RAY DIFFRACTION100
2.1564-2.18720.28396920.257213255X-RAY DIFFRACTION100
2.1872-2.21990.28026930.239213162X-RAY DIFFRACTION100
2.2199-2.25450.27536980.238513214X-RAY DIFFRACTION100
2.2545-2.29150.28126980.242113197X-RAY DIFFRACTION100
2.2915-2.3310.27197210.235513172X-RAY DIFFRACTION99
2.331-2.37330.26456880.225213221X-RAY DIFFRACTION100
2.3733-2.4190.2717030.222513190X-RAY DIFFRACTION99
2.419-2.46830.27076980.22513191X-RAY DIFFRACTION100
2.4683-2.52190.26577040.223713243X-RAY DIFFRACTION100
2.5219-2.58060.26977120.220213186X-RAY DIFFRACTION99
2.5806-2.64510.24866950.210613232X-RAY DIFFRACTION100
2.6451-2.71650.25186960.20913231X-RAY DIFFRACTION100
2.7165-2.79640.2566930.207113255X-RAY DIFFRACTION100
2.7964-2.88660.24267330.204313213X-RAY DIFFRACTION99
2.8866-2.98960.24697240.20213262X-RAY DIFFRACTION100
2.9896-3.10920.23466940.204413237X-RAY DIFFRACTION99
3.1092-3.25050.24586640.204513308X-RAY DIFFRACTION99
3.2505-3.42160.22216760.191713311X-RAY DIFFRACTION99
3.4216-3.63550.20577050.181913285X-RAY DIFFRACTION99
3.6355-3.91550.19247190.167813338X-RAY DIFFRACTION99
3.9155-4.30830.19287100.155413283X-RAY DIFFRACTION99
4.3083-4.92880.15126890.142613440X-RAY DIFFRACTION99
4.9288-6.19880.19417630.172113513X-RAY DIFFRACTION100
6.1988-28.09320.19117220.171213719X-RAY DIFFRACTION98

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