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- PDB-8hap: Crystal structure of thermostable acetaldehyde dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 8hap
TitleCrystal structure of thermostable acetaldehyde dehydrogenase from hyperthermophilic archaeon Sulfolobus tokodaii
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / thermostability / acetaldehyde / aldehyde / dehydrogenase / archaea
Function / homology
Function and homology information


lactaldehyde dehydrogenase (NAD+) activity
Similarity search - Function
: / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE / Chem-NA7 / Aldehyde dehydrogenase family protein
Similarity search - Component
Biological speciesSulfurisphaera tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsMine, S. / Nakabayashi, M. / Ishikawa, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Crystal structure of thermostable acetaldehyde dehydrogenase from the hyperthermophilic archaeon Sulfolobus tokodaii.
Authors: Mine, S. / Nakabayashi, M. / Ishikawa, K.
History
DepositionOct 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1956
Polymers105,0192
Non-polymers1,1764
Water4,810267
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules

A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,39112
Polymers210,0384
Non-polymers2,3538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area23390 Å2
ΔGint-154 kcal/mol
Surface area56930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.075, 75.356, 105.305
Angle α, β, γ (deg.)90.000, 124.640, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-633-

HOH

21A-731-

HOH

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Components

#1: Protein Aldehyde dehydrogenase


Mass: 52509.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurisphaera tokodaii (archaea) / Gene: HA332_07780 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A832TGS5
#2: Chemical ChemComp-NA7 / [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE


Mass: 623.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N5O16P3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ATR / 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100 mM sodium phosphate dibasic/citric acid (pH 4.2), 200 mM sodium chloride, 10% (v/v) polyethylene glycol (PEG) 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.197→86.635 Å / Num. all: 53563 / Num. obs: 53563 / % possible obs: 99 % / Redundancy: 3.4 % / Rpim(I) all: 0.056 / Rrim(I) all: 0.104 / Rsym value: 0.087 / Net I/av σ(I): 7 / Net I/σ(I): 9.9 / Num. measured all: 182293
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.323.30.5881.32504176980.3830.7040.5882.397.7
2.32-2.463.40.4311.72541673680.2730.5110.4313.199.6
2.46-2.633.60.3262.22482969940.2040.3850.3264.299.6
2.63-2.843.50.2243.12285464910.1390.2640.224699.8
2.84-3.113.50.1514.52071660040.0950.1790.1518.599.9
3.11-3.473.20.0897.51736854270.0590.1070.08912.199.7
3.47-4.013.50.055121677147320.0350.0660.05519.298.9
4.01-4.913.40.04115.61365139970.0260.0480.04124.398.4
4.91-6.953.20.03916.6999531580.0260.0470.03920.898.4
6.95-46.5533.30.0313.8565216940.020.0360.0328.895.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PQA

3pqa


Resolution: 2.2→46.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.285 / SU ML: 0.112 / SU R Cruickshank DPI: 0.2264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 2699 5 %RANDOM
Rwork0.168 ---
obs0.1702 50864 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.2 Å2 / Biso mean: 36.577 Å2 / Biso min: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20.01 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.2→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7176 0 72 267 7515
Biso mean--51.67 48.08 -
Num. residues----932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137351
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177360
X-RAY DIFFRACTIONr_angle_refined_deg1.561.6449945
X-RAY DIFFRACTIONr_angle_other_deg1.2891.57816982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0865930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.73822.139346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.709151370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5021554
X-RAY DIFFRACTIONr_chiral_restr0.0710.21019
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021528
LS refinement shellResolution: 2.2→2.254 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.231 184 -
Rwork0.152 3646 -
obs--95.61 %

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