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- PDB-6jnj: Crystal structure of Azospirillum brasilense L-arabinose 1-dehydr... -

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Basic information

Entry
Database: PDB / ID: 6jnj
TitleCrystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase (apo-form)
ComponentsL-arabinose 1-dehydrogenase (NAD(P)(+))
KeywordsOXIDOREDUCTASE / L-arabinose metabolism / NADP-dependent dehydrogenase / Gfo/Idh/MocA protein family
Function / homology
Function and homology information


L-arabinose 1-dehydrogenase [NAD(P)+] / L-arabinose catabolic process / L-arabinose 1-dehydrogenase (NADP+) activity / L-arabinose 1-dehydrogenase (NAD+) activity / galactose 1-dehydrogenase (NADP+) / galactose 1-dehydrogenase (NADP+) activity / D-galactose 1-dehydrogenase / galactose 1-dehydrogenase activity / L-arabinose catabolic process to 2-oxoglutarate / NADP+ binding ...L-arabinose 1-dehydrogenase [NAD(P)+] / L-arabinose catabolic process / L-arabinose 1-dehydrogenase (NADP+) activity / L-arabinose 1-dehydrogenase (NAD+) activity / galactose 1-dehydrogenase (NADP+) / galactose 1-dehydrogenase (NADP+) activity / D-galactose 1-dehydrogenase / galactose 1-dehydrogenase activity / L-arabinose catabolic process to 2-oxoglutarate / NADP+ binding / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD+ binding
Similarity search - Function
Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / L-arabinose 1-dehydrogenase (NAD(P)(+))
Similarity search - Component
Biological speciesAzospirillum brasilense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWatanabe, Y. / Iga, C. / Watanabe, S.
CitationJournal: Febs Lett. / Year: 2019
Title: Structural insights into the catalytic and substrate recognition mechanisms of bacterial l-arabinose 1-dehydrogenase.
Authors: Watanabe, Y. / Iga, C. / Watanabe, Y. / Watanabe, S.
History
DepositionMar 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Nov 22, 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

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Assembly

Deposited unit
A: L-arabinose 1-dehydrogenase (NAD(P)(+))
B: L-arabinose 1-dehydrogenase (NAD(P)(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1754
Polymers67,9852
Non-polymers1902
Water12,881715
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-27 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.700, 63.470, 66.170
Angle α, β, γ (deg.)107.770, 100.700, 115.980
Int Tables number1
Space group name H-MP1

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Components

#1: Protein L-arabinose 1-dehydrogenase (NAD(P)(+)) / D-galactose 1-dehydrogenase


Mass: 33992.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azospirillum brasilense (bacteria) / Gene: araA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q53TZ2, L-arabinose 1-dehydrogenase [NAD(P)+], galactose 1-dehydrogenase (NADP+), D-galactose 1-dehydrogenase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.4 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 115047 / % possible obs: 98.8 % / Redundancy: 3.3 % / Net I/σ(I): 5.47
Reflection shellResolution: 1.5→1.54 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EW6

4ew6


Resolution: 1.5→46.457 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 22.44
RfactorNum. reflection% reflection
Rfree0.2178 5813 5.05 %
Rwork0.1952 --
obs0.1964 115047 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.09 Å2 / Biso mean: 21.3138 Å2 / Biso min: 9.74 Å2
Refinement stepCycle: final / Resolution: 1.5→46.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4727 0 10 715 5452
Biso mean--25.89 31.07 -
Num. residues----613
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.51710.22491870.208836613848100
1.5171-1.53490.22872070.211536153822100
1.5349-1.55360.23261940.211136613855100
1.5536-1.57330.26531840.212135783762100
1.5733-1.5940.24851880.207237503938100
1.594-1.61590.23971870.202535673754100
1.6159-1.63890.23521830.207236663849100
1.6389-1.66340.2421460.210937473893100
1.6634-1.68940.24112110.205236053816100
1.6894-1.71710.24021780.209637013879100
1.7171-1.74670.26331990.220736063805100
1.7467-1.77850.25871690.217236863855100
1.7785-1.81270.25961890.218536993888100
1.8127-1.84970.20161770.218436163793100
1.8497-1.88990.25412150.208335793794100
1.8899-1.93390.25652190.209836833902100
1.9339-1.98220.22332070.204936413848100
1.9822-2.03580.21741910.211736093800100
2.0358-2.09570.25141910.203836853876100
2.0957-2.16340.21912020.204336143816100
2.1634-2.24070.23862180.203936483866100
2.2407-2.33040.22432010.201435973798100
2.3304-2.43650.23911790.209436883867100
2.4365-2.56490.21282220.207436013823100
2.5649-2.72560.25691900.205936483838100
2.7256-2.9360.21321740.19743660383499
2.936-3.23140.21122020.20123586378899
3.2314-3.69880.19572080.17523642385099
3.6988-4.65940.16391960.15313584378099
4.6594-46.47980.19951990.18063611381099

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