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

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Basic information

Entry
Database: PDB / ID: 7cgr
TitleCrystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase E147A mutant (NADP and glycerol 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 / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
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: 2.093 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 / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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

Downloads & links

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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)143,12111
Polymers139,8714
Non-polymers3,2507
Water13,673759
1
A: L-arabinose 1-dehydrogenase (NAD(P)(+))
B: L-arabinose 1-dehydrogenase (NAD(P)(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6066
Polymers69,9352
Non-polymers1,6714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-24 kcal/mol
Surface area24780 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)71,5145
Polymers69,9352
Non-polymers1,5793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-18 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.857, 90.520, 134.693
Angle α, β, γ (deg.)90.000, 101.930, 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


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 759 / 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: 2.55 Å3/Da / Density % sol: 51.81 %
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: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris-HCl pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→49.171 Å / Num. obs: 82746 / % possible obs: 99.6 % / Redundancy: 3.448 % / Biso Wilson estimate: 35.093 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.176 / Χ2: 0.796 / Net I/σ(I): 7.09 / Num. measured all: 559968
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.09-2.223.2810.8691.528587526412261720.6541.0499.1
2.22-2.373.4610.6232.248531124677246480.8150.73799.9
2.37-2.563.4330.4582.997896223024230010.880.54399.9
2.56-2.813.3570.2984.377112821236211850.9380.35699.8
2.81-3.143.6310.1936.956973619251192070.9750.22799.8
3.14-3.623.5330.11311.145938416905168060.9880.13399.4
3.62-4.433.3990.07215.944822214283141860.9930.08599.3
4.43-6.233.6020.0618.923979611094110470.9950.07199.6
6.23-49.1713.5020.04722.5621554618961550.9970.05599.5

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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: 2.093→48.934 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: 2.093→48.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9361 0 168 759 10288
Biso mean--40.17 35.79 -
Num. residues----1216
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0933-2.11710.30851170.2801255897
2.1171-2.1420.31491660.27132598100
2.142-2.16810.31931500.26082588100
2.1681-2.19550.28111220.24252616100
2.1955-2.22440.28061530.23392589100
2.2244-2.25490.27181460.21952593100
2.2549-2.28710.24451180.2142612100
2.2871-2.32120.23451400.21292616100
2.3212-2.35750.28611180.20942631100
2.3575-2.39620.27771540.21482633100
2.3962-2.43750.25461420.22022557100
2.4375-2.48180.24481330.20412644100
2.4818-2.52950.23531370.20792614100
2.5295-2.58120.24411220.21022633100
2.5812-2.63730.24561510.21372591100
2.6373-2.69860.25441460.21362613100
2.6986-2.76610.24051400.19762613100
2.7661-2.84090.24941200.19182645100
2.8409-2.92450.24661320.18552614100
2.9245-3.01890.19641340.18732657100
3.0189-3.12670.22631530.19112594100
3.1267-3.25190.23991510.19072590100
3.2519-3.39990.21451210.18592656100
3.3999-3.57910.19181460.16592621100
3.5791-3.80320.19991570.15892603100
3.8032-4.09670.20021220.15162662100
4.0967-4.50880.16641640.13792630100
4.5088-5.16060.16551360.14492638100
5.1606-6.49940.22181160.18612688100
6.4994-48.9340.19571680.1622674100

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