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- PDB-8k0o: High resolution structure of Dehydroascorbate Reductase from Cenc... -

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Basic information

Entry
Database: PDB / ID: 8k0o
TitleHigh resolution structure of Dehydroascorbate Reductase from Cenchrus Americanus in complex with Acetate in the G-site and Glycerol in the H-site
ComponentsDehydroascorbate reductase
KeywordsOXIDOREDUCTASE / Dehydroascorbate reductase
Function / homology
Function and homology information


ascorbate glutathione cycle / glutathione dehydrogenase (ascorbate) activity / glutathione dehydrogenase (ascorbate) / glutathione transferase activity
Similarity search - Function
Dehydroascorbate reductases DHAR1/2/3/4 / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
ACETATE ION / glutathione dehydrogenase (ascorbate)
Similarity search - Component
Biological speciesCenchrus americanus (bulrush millet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsKhan, W.A. / Arulandu, A.
Funding support India, 3items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)EMR/2017/005066 India
Department of Biotechnology (DBT, India)BT/PR28766/BRB/10/1701/2018 India
Department of Biotechnology (DBT, India)BT/PR28080/BID/7/836/2018 India
CitationJournal: To Be Published
Title: High resolution structure of Dehydroascorbate Reductase from Pennisetum Americanum in complex with Acetate in the G-site and Glycerol in the H-site
Authors: Khan, W.A. / Das, B.K. / Arulandu, A.
History
DepositionJul 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7663
Polymers25,6151
Non-polymers1512
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.389, 70.389, 111.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-565-

HOH

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Components

#1: Protein Dehydroascorbate reductase


Mass: 25615.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cenchrus americanus (bulrush millet) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U5XYA0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100mM SODIUM ACETATE TRIHYDRATE pH 4.6, 2M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.8→19.85 Å / Num. obs: 26638 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.997 / Net I/σ(I): 13.4
Reflection shellResolution: 1.801→1.833 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1333 / CC1/2: 0.808 / % possible all: 99.1

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Processing

Software
NameClassification
PDB-REDOrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→19.24 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.252 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21888 1223 4.7 %RANDOM
Rwork0.18319 ---
obs0.18489 24837 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.734 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0 Å2-0 Å2
2---0.26 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.81→19.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 10 182 1833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0171710
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161622
X-RAY DIFFRACTIONr_angle_refined_deg1.391.8262323
X-RAY DIFFRACTIONr_angle_other_deg0.5141.5673802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6955.046218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22110298
X-RAY DIFFRACTIONr_chiral_restr0.0670.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02313
X-RAY DIFFRACTIONr_mcbond_it2.5742.054850
X-RAY DIFFRACTIONr_mcbond_other2.5562.052849
X-RAY DIFFRACTIONr_mcangle_it3.3263.0651061
X-RAY DIFFRACTIONr_mcangle_other3.3293.0681062
X-RAY DIFFRACTIONr_scbond_it3.6732.388860
X-RAY DIFFRACTIONr_scbond_other3.6772.391861
X-RAY DIFFRACTIONr_scangle_other5.2433.4291260
X-RAY DIFFRACTIONr_long_range_B_refined7.24328.9031965
X-RAY DIFFRACTIONr_long_range_B_other7.10626.2191899
LS refinement shellResolution: 1.815→1.862 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 91 -
Rwork0.273 1778 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: -14.901 Å / Origin y: 32.02 Å / Origin z: 0.597 Å
111213212223313233
T0.0844 Å20.0252 Å2-0.0105 Å2-0.1201 Å2-0.022 Å2--0.0084 Å2
L2.7179 °21.0761 °2-0.7635 °2-1.7714 °2-0.9191 °2--2.1192 °2
S-0.0997 Å °0.0889 Å °0.0299 Å °-0.064 Å °0.0695 Å °-0.0584 Å °0.0653 Å °0.0136 Å °0.0302 Å °

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