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

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Basic information

Entry
Database: PDB / ID: 7buz
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 / homologyFLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesCenchrus americanus (bulrush millet)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.288 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: To Be Published
Title: Crystal structure of Pennisetum glaucum monodehydroascorbate reductase
Authors: Sonkar, K.S. / Arulandu, A.
History
DepositionApr 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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: Pennisetum glaucum monodehydroascorbate reductase
B: Pennisetum glaucum monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5846
Polymers93,6862
Non-polymers2,8984
Water9,530529
1
A: Pennisetum glaucum monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2923
Polymers46,8431
Non-polymers1,4492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-7 kcal/mol
Surface area17740 Å2
MethodPISA
2
B: Pennisetum glaucum monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2923
Polymers46,8431
Non-polymers1,4492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-7 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.572, 83.460, 132.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pennisetum glaucum monodehydroascorbate reductase


Mass: 46843.133 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium acetate trihydrate 0.1 M Sodium cacodylate trihydrate pH 6.5 30% w/v Polyethylene glycol 8,000
PH range: 6.2 - 6.8

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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: Jan 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.288→70.675 Å / Num. obs: 41184 / % possible obs: 99.98 % / Redundancy: 15.7 % / CC1/2: 0.996 / Net I/σ(I): 2.18
Reflection shellResolution: 2.288→2.327 Å / Num. unique obs: 41184 / CC1/2: 0.996 / Rpim(I) all: 0.066

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Processing

Software
NameVersionClassification
HKL-2000data reduction
BUSTER2.10.3 (19-MAR-2020)refinement
PDB_EXTRACT3.25data extraction
PHENIX1.15-3459-000model building
BALBES1.0.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5jci

5jci


Resolution: 2.288→70.67 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.884 / SU R Cruickshank DPI: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.37 / SU Rfree Blow DPI: 0.242 / SU Rfree Cruickshank DPI: 0.237
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 2052 4.98 %RANDOM
Rwork0.1868 ---
obs0.1898 41177 100 %-
Displacement parametersBiso max: 66.36 Å2 / Biso mean: 30.99 Å2 / Biso min: 13.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.1979 Å20 Å20 Å2
2--5.0811 Å20 Å2
3----6.2791 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.288→70.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6496 0 160 529 7185
Biso mean--29.66 35.91 -
Num. residues----866
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2285SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1259HARMONIC5
X-RAY DIFFRACTIONt_it6819HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion895SEMIHARMONIC5
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_contact6208SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6857HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg9333HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion16.96
LS refinement shellResolution: 2.29→2.3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2772 37 4.49 %
Rwork0.2245 787 -
all0.227 824 -
obs--100 %

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