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- PDB-7f8s: Pennisetum glaucum (Pearl millet) dehydroascorbate reductase (DHA... -

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Basic information

Entry
Database: PDB / ID: 7f8s
TitlePennisetum glaucum (Pearl millet) dehydroascorbate reductase (DHAR) with catalytic cysteine (Cy20) in sulphenic and sulfinic acid forms.
Components(Dehydroascorbate reductaseGlutathione dehydrogenase (ascorbate)) x 2
KeywordsOXIDOREDUCTASE / Pennisetum glaucum / DHAR / Dehydroascorbate reductase / sulphenic acid / sulfinic acid / cysteine oxidation
Function / homology
Function and homology information


ascorbate glutathione cycle / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
glutathione dehydrogenase (ascorbate)
Similarity search - Component
Biological speciesCenchrus americanus (bulrush millet)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsDas, B.K. / Kumar, A. / Sreeshma, N.S. / Arockiasamy, A.
Funding support India, 3items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR28080/BID/7/836/2018 India
Department of Biotechnology (DBT, India)BT/PR28766/BRB/10/1701/2018 India
Department of Science & Technology (DST, India)EMR/2017/005066 India
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Comparative kinetic analysis of ascorbate (Vitamin-C) recycling dehydroascorbate reductases from plants and humans.
Authors: Das, B.K. / Kumar, A. / Sreekumar, S.N. / Ponraj, K. / Gadave, K. / Kumar, S. / Murali Achary, V.M. / Ray, P. / Reddy, M.K. / Arockiasamy, A.
#1: Journal: Biochem Biophys Res Commun / Year: 2016
Title: Non-native ligands define the active site of Pennisetum glaucum (L.) R. Br dehydroascorbate reductase.
Authors: Krishna Das, B. / Kumar, A. / Maindola, P. / Mahanty, S. / Jain, S.K. / Reddy, M.K. / Arockiasamy, A.
History
DepositionJul 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dehydroascorbate reductase
B: Dehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,14311
Polymers51,2792
Non-polymers8659
Water1,54986
1
A: Dehydroascorbate reductase
hetero molecules

B: Dehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,14311
Polymers51,2792
Non-polymers8659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x+1/2,-y+1/2,-z+1/41
Buried area2800 Å2
ΔGint-118 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.561, 97.561, 109.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Dehydroascorbate reductase / Glutathione dehydrogenase (ascorbate)


Mass: 25631.301 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, glutathione dehydrogenase (ascorbate)
#2: Protein Dehydroascorbate reductase / Glutathione dehydrogenase (ascorbate)


Mass: 25647.301 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, glutathione dehydrogenase (ascorbate)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.53 Å3/Da / Density % sol: 51.44 % / Description: Bipyramidal crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1M Sodium acetate pH 4.6, 2.0M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 16093 / % possible obs: 99.1 % / Redundancy: 13.6 % / Biso Wilson estimate: 50.44 Å2 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.042 / Rrim(I) all: 0.157 / Χ2: 0.675 / Net I/σ(I): 4.3 / Num. measured all: 219205
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.63-2.68120.67670.8150.1760.6260.57597.8
2.68-2.7212.70.5877760.8920.1670.6110.57798.2
2.72-2.7813.10.5137810.9270.1430.5330.55299.1
2.78-2.8313.50.4847950.9360.1340.5030.55698.6
2.83-2.8913.50.4297670.950.1180.4460.56298.5
2.89-2.9613.70.3827910.9570.1040.3960.58198.6
2.96-3.0413.50.3247870.9710.0890.3360.68398.7
3.04-3.1213.80.287940.9820.0760.290.60199
3.12-3.2113.80.2547880.9850.0690.2640.68198.9
3.21-3.3113.80.2247860.9880.0610.2320.65299.2
3.31-3.43140.1898010.990.0510.1960.6599.4
3.43-3.5714.10.167950.9930.0430.1660.66599.5
3.57-3.7314.10.1388120.9960.0370.1430.72899.5
3.73-3.9314.10.1238060.9960.0330.1270.73599.3
3.93-4.1714.10.1138110.9970.0310.1170.71499.8
4.17-4.514.10.1078030.9970.0290.1110.86199.5
4.5-4.9514.10.1038350.9970.0280.1060.71199.8
4.95-5.6613.90.1028240.9970.0280.1060.70799.8
5.66-7.1313.60.1038510.9980.0280.1070.68599.6
7.13-5012.80.0529230.9990.0150.0540.94199

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-APR-2021)refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
BALBESphasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EVO

5evo


Resolution: 2.63→48.78 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 0.62 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.713 / SU Rfree Blow DPI: 0.307 / SU Rfree Cruickshank DPI: 0.306
RfactorNum. reflection% reflectionSelection details
Rfree0.253 655 4.08 %RANDOM
Rwork0.205 ---
obs0.207 16072 99.3 %-
Displacement parametersBiso mean: 35.78 Å2
Baniso -1Baniso -2Baniso -3
1-4.0312 Å20 Å20 Å2
2--4.0312 Å20 Å2
3----8.0623 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.63→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 45 86 3379
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093371HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.054596HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1094SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes549HARMONIC5
X-RAY DIFFRACTIONt_it3371HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion18.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion434SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2855SEMIHARMONIC4
LS refinement shellResolution: 2.63→2.66 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2265 22 4.37 %
Rwork0.248 481 -
obs--97.07 %

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