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- PDB-7bvi: Crystal structure of Pennisetum glaucum monodehydroascorbate reductase -

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Basic information

Entry
Database: PDB / ID: 7bvi
TitleCrystal structure of Pennisetum glaucum monodehydroascorbate reductase
ComponentsPennisetum glaucum monodehydroascorbate reductase
KeywordsOXIDOREDUCTASE / Nucleotide Binding / Oxidoreductase Activity / Monodehydroascorbate Reductase (nadh) Activity / Flavin Adenine Dinucleotide Binding
Function / homologyACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesCenchrus americanus (bulrush millet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.391 Å
AuthorsSonkar, K.S. / Arulandu, A. / Achary, M.M. / Reddy, M.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)No.BT/PR18774/BIC/101/454/2016 India
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Biochemical and structural characterization of a robust and thermostable ascorbate recycling monodehydroascorbate reductase (MDHAR) from stress adapted pearl millet.
Authors: Sonkar, K.S. / Achary, V.M.M. / Sahoo, S. / Reddy, M.K. / Arockiasamy, A.
History
DepositionApr 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author / database_2
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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: Pennisetum glaucum monodehydroascorbate reductase
B: Pennisetum glaucum monodehydroascorbate reductase
C: Pennisetum glaucum monodehydroascorbate reductase
D: Pennisetum glaucum monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,75112
Polymers187,3734
Non-polymers3,3788
Water14,394799
1
A: Pennisetum glaucum monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6883
Polymers46,8431
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-6 kcal/mol
Surface area17510 Å2
MethodPISA
2
B: Pennisetum glaucum monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6883
Polymers46,8431
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-6 kcal/mol
Surface area17580 Å2
MethodPISA
3
C: Pennisetum glaucum monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6883
Polymers46,8431
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-5 kcal/mol
Surface area17740 Å2
MethodPISA
4
D: Pennisetum glaucum monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6883
Polymers46,8431
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-6 kcal/mol
Surface area17460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.959, 79.357, 91.769
Angle α, β, γ (deg.)96.000, 97.290, 112.410
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Pennisetum glaucum monodehydroascorbate reductase


Mass: 46843.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cenchrus americanus (bulrush millet) / Gene: MDHAR / Plasmid: pETM30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: monodehydroascorbate reductase (NADH)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 799 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M) Sodium acetate trihydrate 0.1 M Sodium cacodylate trihydrate pH 6.5 30% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 27, 2018 / Details: insertion device (ID)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.391→72.34 Å / Num. obs: 61346 / % possible obs: 92.17 % / Redundancy: 3.9 % / Biso Wilson estimate: 37.89 Å2 / CC1/2: 0.993 / Net I/σ(I): 2.17
Reflection shellResolution: 2.391→2.432 Å / Num. unique obs: 237394 / CC1/2: 0.993 / Rrim(I) all: 0.12

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
PDB_EXTRACT3.25data extraction
BALBES1.0.0phasing
PHENIX1.15-3459-000model building
ARP/wARP7.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5jci

5jci


Resolution: 2.391→72.34 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.887 / SU R Cruickshank DPI: 0.641 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.619 / SU Rfree Blow DPI: 0.261 / SU Rfree Cruickshank DPI: 0.266
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3023 4.93 %RANDOM
Rwork0.1686 ---
obs0.1715 61346 92.2 %-
Displacement parametersBiso max: 64.26 Å2 / Biso mean: 26.31 Å2 / Biso min: 6.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.1352 Å24.8247 Å22.2519 Å2
2--5.045 Å2-0.7748 Å2
3----3.9098 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2.391→72.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12869 0 228 799 13896
Biso mean--21.1 28.57 -
Num. residues----1728
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4388SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2401HARMONIC5
X-RAY DIFFRACTIONt_it13401HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1753SEMIHARMONIC5
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_contact11616SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13401HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg18226HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion16.4
LS refinement shellResolution: 2.391→2.41 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.285 64 5.22 %
Rwork0.1878 1163 -
obs--94.59 %

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