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- PDB-5evo: Structure of Dehydroascrobate Reductase from Pennisetum Americanu... -

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Basic information

Entry
Database: PDB / ID: 5evo
TitleStructure of Dehydroascrobate Reductase from Pennisetum Americanum in complex with two non-native ligands, Acetate in the G-site and Glycerol in the H-site
ComponentsDehydroascorbate reductase
KeywordsOXIDOREDUCTASE / APO(NATIVE) / DHAR / Non-Native ligands / Acetate (G-site) / Glycerol (H-site)
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 S-transferase, N-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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. ...Dehydroascorbate reductases DHAR1/2/3/4 / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-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 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Dehydroascorbate reductase
Similarity search - Component
Biological speciesCenchrus americanus (bulrush millet)
MethodX-RAY DIFFRACTION / Resolution: 2.51 Å
AuthorsKumar, A.O. / Das, B.K. / Arockiasamy, A.
CitationJournal: 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
DepositionNov 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 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 1.2Mar 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)23,8773
Polymers23,7261
Non-polymers1512
Water1,15364
1
A: Dehydroascorbate reductase
hetero molecules

A: Dehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7556
Polymers47,4522
Non-polymers3024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area2250 Å2
ΔGint-12 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.494, 69.494, 111.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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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.) Cenchrus americanus (bulrush millet) / Production host: Escherichia coli (E. coli)
References: UniProt: U5XYA0, glutathione dehydrogenase (ascorbate)
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: SODIUM ACETATE, 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: Aug 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 9893 / % possible obs: 99.4 % / Redundancy: 8.8 % / Biso Wilson estimate: 62.74 Å2 / Net I/σ(I): 28.99

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementResolution: 2.51→49.14 Å / Cor.coef. Fo:Fc: 0.9376 / Cor.coef. Fo:Fc free: 0.9103 / SU R Cruickshank DPI: 0.371 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.417 / SU Rfree Blow DPI: 0.257 / SU Rfree Cruickshank DPI: 0.252
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 473 4.81 %RANDOM
Rwork0.196 ---
obs0.1981 9838 99.48 %-
Displacement parametersBiso mean: 52.89 Å2
Baniso -1Baniso -2Baniso -3
1--2.7708 Å20 Å20 Å2
2---2.7708 Å20 Å2
3---5.5417 Å2
Refine analyzeLuzzati coordinate error obs: 0.316 Å
Refinement stepCycle: LAST / Resolution: 2.51→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 10 64 1705
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091686HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.122293HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d551SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes242HARMONIC5
X-RAY DIFFRACTIONt_it1686HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.75
X-RAY DIFFRACTIONt_other_torsion17.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion219SEMIHARMONIC5
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_contact1991SEMIHARMONIC4
LS refinement shellResolution: 2.51→2.81 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2802 134 4.99 %
Rwork0.2119 2550 -
all0.2155 2684 -
obs--98.28 %

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