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- PDB-7cov: Potato D-enzyme, native (substrate free) -

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Basic information

Entry
Database: PDB / ID: 7cov
TitlePotato D-enzyme, native (substrate free)
Components4-alpha-glucanotransferase, chloroplastic/amyloplastic
KeywordsTRANSFERASE / D-enzyme / disproportionating enzyme / potato / cycloamylose / Solanum tuberosum / PLANT PROTEIN
Function / homology
Function and homology information


amyloplast / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / beta-maltose 4-alpha-glucanotransferase activity / chloroplast / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 77 / 4-alpha-glucanotransferase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
4-alpha-glucanotransferase, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsUnno, H. / Imamura, K.
CitationJournal: Protein Sci. / Year: 2020
Title: Structural analysis and reaction mechanism of the disproportionating enzyme (D-enzyme) from potato.
Authors: Imamura, K. / Matsuura, T. / Nakagawa, A. / Kitamura, S. / Kusunoki, M. / Takaha, T. / Unno, H.
History
DepositionAug 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
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
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-alpha-glucanotransferase, chloroplastic/amyloplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,79810
Polymers65,0211
Non-polymers7779
Water10,899605
1
A: 4-alpha-glucanotransferase, chloroplastic/amyloplastic
hetero molecules

A: 4-alpha-glucanotransferase, chloroplastic/amyloplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,59620
Polymers130,0432
Non-polymers1,55418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8870 Å2
ΔGint-48 kcal/mol
Surface area43950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.869, 120.535, 174.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 4-alpha-glucanotransferase, chloroplastic/amyloplastic / Amylomaltase / Disproportionating enzyme / D-enzyme


Mass: 65021.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Gene: DPEP / Production host: Escherichia coli (E. coli) / References: UniProt: Q06801, 4-alpha-glucanotransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 273 K / Method: vapor diffusion / Details: 12% PEG 8000, 100 mM HEPES (pH 7.6), 100 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 26, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→35.36 Å / Num. obs: 49562 / % possible obs: 99.2 % / Redundancy: 7.3 % / CC1/2: 1 / Rrim(I) all: 0.032 / Net I/σ(I): 44.2
Reflection shellResolution: 2→2.11 Å / Num. unique obs: 7039 / CC1/2: 0.996 / Rrim(I) all: 0.092

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→35.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1878 2503 5.052 %
Rwork0.1505 47044 -
all0.152 --
obs-49547 98.955 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.523 Å2
Baniso -1Baniso -2Baniso -3
1--0.003 Å20 Å20 Å2
2--0.005 Å20 Å2
3----0.002 Å2
Refinement stepCycle: LAST / Resolution: 2→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4183 0 49 605 4837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134387
X-RAY DIFFRACTIONr_bond_other_d0.0340.0174023
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.6365941
X-RAY DIFFRACTIONr_angle_other_deg2.4741.5789357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5445522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44222.449245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77315726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1391530
X-RAY DIFFRACTIONr_chiral_restr0.0930.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024870
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02940
X-RAY DIFFRACTIONr_nbd_refined0.2160.21002
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.23801
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22195
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21728
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2507
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1470.217
X-RAY DIFFRACTIONr_nbd_other0.220.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.232
X-RAY DIFFRACTIONr_mcbond_it3.0342.5072097
X-RAY DIFFRACTIONr_mcbond_other32.5072090
X-RAY DIFFRACTIONr_mcangle_it4.3653.7452612
X-RAY DIFFRACTIONr_mcangle_other4.3663.7462613
X-RAY DIFFRACTIONr_scbond_it3.762.9052290
X-RAY DIFFRACTIONr_scbond_other3.7592.9072291
X-RAY DIFFRACTIONr_scangle_it5.7584.1833329
X-RAY DIFFRACTIONr_scangle_other5.7574.1853330
X-RAY DIFFRACTIONr_lrange_it8.41231.5385465
X-RAY DIFFRACTIONr_lrange_other8.24330.7885280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.211770.173341X-RAY DIFFRACTION95.9629
2.052-2.1080.1871660.1483354X-RAY DIFFRACTION99.0155
2.108-2.1690.1791980.1493233X-RAY DIFFRACTION99.0188
2.169-2.2360.1731280.1423220X-RAY DIFFRACTION98.9654
2.236-2.3090.1861650.1443075X-RAY DIFFRACTION99.2647
2.309-2.390.1831440.1432991X-RAY DIFFRACTION99.1775
2.39-2.480.1881390.142907X-RAY DIFFRACTION99.4775
2.48-2.5820.2121750.1412769X-RAY DIFFRACTION99.3923
2.582-2.6960.1841490.1422657X-RAY DIFFRACTION99.4683
2.696-2.8280.1881770.1482517X-RAY DIFFRACTION99.5933
2.828-2.9810.1891210.1442463X-RAY DIFFRACTION99.6914
2.981-3.1610.207990.1512359X-RAY DIFFRACTION99.716
3.161-3.3790.1891310.1552138X-RAY DIFFRACTION99.6487
3.379-3.6490.2111020.1672069X-RAY DIFFRACTION99.6329
3.649-3.9970.165720.1481902X-RAY DIFFRACTION99.697
3.997-4.4680.158910.1391711X-RAY DIFFRACTION99.2291
4.468-5.1560.1481050.1241480X-RAY DIFFRACTION99.0625
5.156-6.310.274760.1811305X-RAY DIFFRACTION99.7112
6.31-8.90.167550.1781015X-RAY DIFFRACTION98.4361
8.9-35.360.196330.198538X-RAY DIFFRACTION88.5271

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