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- PDB-7cgq: Crystal structure of Azospirillum brasilense L-arabinose 1-dehydr... -

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Basic information

Entry
Database: PDB / ID: 7cgq
TitleCrystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase E147A mutant (NADP and L-arabinose bound 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 / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor ...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 / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NADP+ binding / NAD+ binding
Similarity search - Function
Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
alpha-L-arabinopyranose / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-arabinose 1-dehydrogenase (NAD(P)(+))
Similarity search - Component
Biological speciesAzospirillum brasilense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.208 Å
AuthorsYoshiwara, K. / Watanabe, Y. / Watanabe, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of bacterial L-arabinose 1-dehydrogenase in complex with L-arabinose and NADP+
Authors: Yoshiwara, K. / Watanabe, S. / Watanabe, Y.
History
DepositionJul 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 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)(+))
C: L-arabinose 1-dehydrogenase (NAD(P)(+))
D: L-arabinose 1-dehydrogenase (NAD(P)(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,9959
Polymers139,8714
Non-polymers3,1245
Water6,161342
1
A: L-arabinose 1-dehydrogenase (NAD(P)(+))
B: L-arabinose 1-dehydrogenase (NAD(P)(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5725
Polymers69,9352
Non-polymers1,6373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-20 kcal/mol
Surface area25100 Å2
MethodPISA
2
C: L-arabinose 1-dehydrogenase (NAD(P)(+))
D: L-arabinose 1-dehydrogenase (NAD(P)(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4224
Polymers69,9352
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-16 kcal/mol
Surface area25410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.078, 92.096, 135.133
Angle α, β, γ (deg.)90.000, 102.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34967.727 Da / Num. of mol.: 4 / Mutation: E147A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azospirillum brasilense (bacteria) / Gene: araA / Production host: Escherichia coli (E. coli)
References: UniProt: Q53TZ2, L-arabinose 1-dehydrogenase [NAD(P)+], galactose 1-dehydrogenase (NADP+), D-galactose 1-dehydrogenase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-ARA / alpha-L-arabinopyranose / alpha-L-arabinose / L-arabinose / arabinose / Arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinopyranoseCOMMON NAMEGMML 1.0
a-L-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.91 %
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 / pH: 7
Details: 0.2M Ammonium citrate tribasic pH 7.0, 18.5% PEG 3350

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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: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.208→50 Å / Num. obs: 82746 / % possible obs: 95.7 % / Redundancy: 1.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.084 / Net I/σ(I): 6.45
Reflection shellResolution: 2.21→2.34 Å / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1 / Num. unique obs: 21839 / CC1/2: 0.664 / Rrim(I) all: 0.798

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Processing

Software
NameVersionClassification
XDSdata processing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JNK

6jnk


Resolution: 2.208→49.385 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.2 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2221 4175 5.05 %
Rwork0.1852 78571 -
obs0.1871 82746 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.98 Å2 / Biso mean: 32.0001 Å2 / Biso min: 14.51 Å2
Refinement stepCycle: final / Resolution: 2.208→49.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9366 0 160 342 9868
Biso mean--56.86 42.79 -
Num. residues----1217
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.208-2.23660.38031540.3547253497
2.2366-2.26720.34871280.3439256498
2.2672-2.29960.38431470.3163262699
2.2996-2.33390.33321370.2912261399
2.3339-2.37040.32721550.2948254899
2.3704-2.40930.35061030.2899268199
2.4093-2.45080.32961470.2868258099
2.4508-2.49540.30541390.2708262299
2.4954-2.54340.32581400.2587257499
2.5434-2.59530.30691240.2552263599
2.5953-2.65170.33021510.2603258899
2.6517-2.71340.32071360.2683263899
2.7134-2.78120.27711200.2405260399
2.7812-2.85640.28691380.2308265899
2.8564-2.94050.26581610.22922569100
2.9405-3.03540.26271270.2228265799
3.0354-3.14380.2751230.22352664100
3.1438-3.26970.26731530.22582586100
3.2697-3.41850.26461800.2123260599
3.4185-3.59860.26031280.196260899
3.5986-3.8240.25371200.1805266399
3.824-4.11920.19671430.1729262099
4.1192-4.53340.17571190.1504265299
4.5334-5.18880.19531730.1601261299
5.1888-6.5350.23111340.1937268599
6.535-49.3850.21351360.1699269799

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