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- PDB-5iqy: Structure of apo-Dehydroascorbate Reductase from Pennisetum Glauc... -

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Basic information

Entry
Database: PDB / ID: 5iqy
TitleStructure of apo-Dehydroascorbate Reductase from Pennisetum Glaucum phased by Iodide-SAD method
ComponentsDehydroascorbate reductase
KeywordsOXIDOREDUCTASE / Dehydroascorbate Reductase / Iodide-SAD method
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, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Dehydroascorbate reductases DHAR1/2/3/4 / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / glutathione dehydrogenase (ascorbate)
Similarity search - Component
Biological speciesPennisetum americanum (bulrush millet)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.4 Å
AuthorsDas, B.K. / Kumar, A. / Manidola, P. / Arockiasamy, A.
Funding support India, 1items
OrganizationGrant numberCountry
DBT India
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Non-native ligands define the active site of Pennisetum glaucum (L.) R. Br dehydroascorbate reductase
Authors: Das, B.K. / Kumar, A. / Maindola, P. / Mahanty, S. / Jain, S.K. / Reddy, M.K. / Arockiasamy, A.
History
DepositionMar 11, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Oct 4, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Dehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,02627
Polymers23,7261
Non-polymers3,30026
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-9 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.890, 132.080, 97.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Dehydroascorbate reductase


Mass: 23726.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pennisetum americanum (bulrush millet)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: U5XYA0, glutathione dehydrogenase (ascorbate)
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6 / Details: Tris, Lithium Sulfate, Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→66.05 Å / Num. obs: 10732 / % possible obs: 99.9 % / Redundancy: 27.3 % / Biso Wilson estimate: 44.73 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 32
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.45

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→48.78 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.896 / SU R Cruickshank DPI: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.315 / SU Rfree Blow DPI: 0.227 / SU Rfree Cruickshank DPI: 0.223
RfactorNum. reflection% reflectionSelection details
Rfree0.234 946 8.83 %RANDOM
Rwork0.184 ---
obs0.188 10710 99.8 %-
Displacement parametersBiso mean: 42.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.8121 Å20 Å20 Å2
2---8.2062 Å20 Å2
3---6.3942 Å2
Refine analyzeLuzzati coordinate error obs: 0.282 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 26 95 1719
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091644HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.062243HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d533SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes236HARMONIC5
X-RAY DIFFRACTIONt_it1644HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion17.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion217SEMIHARMONIC5
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_contact2030SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.68 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2482 289 9.76 %
Rwork0.189 2673 -
all0.1948 2962 -
obs--99.53 %
Refinement TLS params.Method: refined / Origin x: 0.0876 Å / Origin y: 12.3115 Å / Origin z: 40.271 Å
111213212223313233
T-0.0024 Å2-0.0306 Å2-0.0531 Å2-0.0112 Å20.0019 Å2--0.0564 Å2
L2.3597 °20.0275 °20.0596 °2-2.6475 °2-1.8239 °2--5.6609 °2
S-0.0108 Å °0.0157 Å °0.1429 Å °0.1915 Å °-0.1233 Å °0.0349 Å °-0.3772 Å °0.187 Å °0.1341 Å °
Refinement TLS groupSelection details: { A|3 - A|213 }

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