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- PDB-6pnu: Crystal structure of native DauA -

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Basic information

Entry
Database: PDB / ID: 6pnu
TitleCrystal structure of native DauA
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
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, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal ...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, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aldehyde dehydrogenase
Similarity search - Component
Biological speciesPseudoalteromonas fuliginea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsPluvinage, B. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Commun Biol / Year: 2019
Title: Insights into the kappa / iota-carrageenan metabolism pathway of some marinePseudoalteromonasspecies.
Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. ...Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. / Van Hamme, J. / Boraston, A.B.
History
DepositionJul 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 15, 2020Group: 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.identifier_ORCID / _citation_author.name
Revision 1.3Oct 11, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,75024
Polymers213,5094
Non-polymers1,24120
Water13,890771
1
A: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules

B: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,75024
Polymers213,5094
Non-polymers1,24120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area16590 Å2
ΔGint7 kcal/mol
Surface area63480 Å2
MethodPISA
2
A: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,25110
Polymers106,7552
Non-polymers4978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint7 kcal/mol
Surface area33140 Å2
MethodPISA
3
B: Aldehyde dehydrogenase
hetero molecules

D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,49914
Polymers106,7552
Non-polymers74512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area7420 Å2
ΔGint15 kcal/mol
Surface area32950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.880, 137.800, 108.870
Angle α, β, γ (deg.)90.000, 109.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aldehyde dehydrogenase /


Mass: 53377.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas fuliginea (bacteria) / Gene: DC53_13140 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A063KJS9*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 771 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.3 M ammonium fluoride, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→75.664 Å / Num. obs: 153728 / % possible obs: 99.4 % / Redundancy: 5.3 % / CC1/2: 0.984 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.075 / Net I/σ(I): 5.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.656 / Num. unique obs: 7558 / CC1/2: 0.818 / Rpim(I) all: 0.346 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JZ4

3jz4


Resolution: 2→75.664 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.53
RfactorNum. reflection% reflection
Rfree0.2589 7532 4.9 %
Rwork0.2216 --
obs0.2234 153579 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.09 Å2 / Biso mean: 30.7692 Å2 / Biso min: 12.88 Å2
Refinement stepCycle: final / Resolution: 2→75.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14320 0 80 771 15171
Biso mean--39.5 33.17 -
Num. residues----1922
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02270.33632400.2947489899
2.0227-2.04650.3162420.2723478499
2.0465-2.07150.29472630.2643484699
2.0715-2.09770.33292250.2535479899
2.0977-2.12530.31712730.2568486099
2.1253-2.15440.28312390.2479479799
2.1544-2.18520.30632460.2399488899
2.1852-2.21780.2762510.2418480599
2.2178-2.25250.29542700.2384485299
2.2525-2.28940.30312650.2366480999
2.2894-2.32890.29392640.2359483499
2.3289-2.37130.31612360.2352488599
2.3713-2.41690.29232550.2321481899
2.4169-2.46620.27672580.2285487599
2.4662-2.51980.25452550.23482899
2.5198-2.57840.28452200.2276489699
2.5784-2.64290.27422580.2253486599
2.6429-2.71440.28612420.2268489199
2.7144-2.79430.27852700.2298484299
2.7943-2.88450.29232430.23394873100
2.8845-2.98760.31282490.2414896100
2.9876-3.10720.28312650.23874866100
3.1072-3.24860.25622340.22514896100
3.2486-3.41990.23722280.22294936100
3.4199-3.63410.24662300.22654927100
3.6341-3.91470.2532350.20864921100
3.9147-4.30860.23372450.19744924100
4.3086-4.9320.2072790.18894882100
4.932-6.21340.21062780.20194915100
6.2134-75.6640.21232740.1915494099

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