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- PDB-4twl: Crystal structure of dioscorin complexed with ascorbate -

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Basic information

Entry
Database: PDB / ID: 4twl
TitleCrystal structure of dioscorin complexed with ascorbate
ComponentsDioscorin 5
KeywordsPLANT PROTEIN / dioscorin / ascorbate / carbonic anhydrase / dehydroascorbate reductase
Function / homology
Function and homology information


response to oxygen radical / monodehydroascorbate reductase (NADH) / monodehydroascorbate reductase (NADH) activity / cellular response to carbon dioxide / carbon utilization / nutrient reservoir activity / negative regulation of endopeptidase activity / L-ascorbic acid binding / cellular oxidant detoxification / antioxidant activity ...response to oxygen radical / monodehydroascorbate reductase (NADH) / monodehydroascorbate reductase (NADH) activity / cellular response to carbon dioxide / carbon utilization / nutrient reservoir activity / negative regulation of endopeptidase activity / L-ascorbic acid binding / cellular oxidant detoxification / antioxidant activity / positive regulation of phagocytosis / carbonic anhydrase / carbonate dehydratase activity / serine-type endopeptidase inhibitor activity / one-carbon metabolic process / positive regulation of gene expression / protein homodimerization activity / zinc ion binding
Similarity search - Function
Carbonic anhydrase, prokaryotic-like / Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
ASCORBIC ACID / Dioscorin dioA3
Similarity search - Component
Biological speciesDioscorea japonica (Japanese yam)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.11 Å
AuthorsXue, Y.L. / Miyakawa, T. / Nakamura, A. / Tanokura, M.
Funding support Japan, China, 4items
OrganizationGrant numberCountry
High Energy Accelerator Research Organization2011G605 Japan
Targeted Proteins Research Program (TPRP) of the Ministry of Education, Culture, Sports, Science and Technology of Japan Japan
National Natural Science Foundation of China31201285 China
Scientific Research Foundation for the Returned Overseas Chinese Scholars2013693 China
CitationJournal: Mol Plant / Year: 2015
Title: Yam Tuber Storage Protein Reduces Plant Oxidants Using the Coupled Reactions as Carbonic Anhydrase and Dehydroascorbate Reductase
Authors: Xue, Y.L. / Miyakawa, T. / Nakamura, A. / Hatano, K. / Sawano, Y. / Tanokura, M.
History
DepositionJul 1, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: Dioscorin 5
B: Dioscorin 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2689
Polymers56,4352
Non-polymers8337
Water1,67593
1
A: Dioscorin 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5864
Polymers28,2181
Non-polymers3683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dioscorin 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6825
Polymers28,2181
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.505, 157.103, 83.485
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 Dioscorin 5


Mass: 28217.619 Da / Num. of mol.: 2 / Fragment: UNP residues 26-271 / Mutation: E9D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscorea japonica (Japanese yam) / Gene: dio5 / Production host: Escherichia coli (E. coli) / References: UniProt: A7MAQ2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: BICINE, PEG400, ammonium sulfate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→20 Å / Num. obs: 31531 / % possible obs: 99 % / Redundancy: 6.5 % / Rsym value: 0.045 / Net I/σ(I): 51.6

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementResolution: 2.11→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.724 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26604 1598 5.1 %RANDOM
Rwork0.20132 ---
obs0.20476 29858 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.186 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---1.71 Å2-0 Å2
3---1.58 Å2
Refinement stepCycle: 1 / Resolution: 2.11→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3849 0 49 93 3991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193983
X-RAY DIFFRACTIONr_bond_other_d0.0020.023675
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.9485386
X-RAY DIFFRACTIONr_angle_other_deg0.89338425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2885473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09424.17223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44615670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6291536
X-RAY DIFFRACTIONr_chiral_restr0.120.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021001
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5663.9371898
X-RAY DIFFRACTIONr_mcbond_other3.5643.9351897
X-RAY DIFFRACTIONr_mcangle_it4.815.8812369
X-RAY DIFFRACTIONr_mcangle_other4.815.8832370
X-RAY DIFFRACTIONr_scbond_it4.3544.4012084
X-RAY DIFFRACTIONr_scbond_other4.3394.3972081
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3656.4293016
X-RAY DIFFRACTIONr_long_range_B_refined8.57631.1684346
X-RAY DIFFRACTIONr_long_range_B_other8.57531.1784347
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.111→2.166 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 118 -
Rwork0.254 1951 -
obs--88.99 %

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