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- PDB-6lx2: Potato D-enzyme complexed with CA26 -

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Basic information

Entry
Database: PDB / ID: 6lx2
TitlePotato D-enzyme complexed with CA26
Components4-alpha-glucanotransferase, chloroplastic/amyloplastic
KeywordsTRANSFERASE / D-enzyme / disproportionating enzyme / potato / cycloamylose / Solanum tuberosum / PLANT PROTEIN
Function / homologyGlycoside hydrolase, family 77 / 4-alpha-glucanotransferase / amyloplast / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / chloroplast / Glycoside hydrolase superfamily / carbohydrate metabolic process / 4-alpha-glucanotransferase, chloroplastic/amyloplastic
Function and homology information
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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
DepositionFeb 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: 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
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: 4-alpha-glucanotransferase, chloroplastic/amyloplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8893
Polymers59,2241
Non-polymers1,6662
Water5,188288
1
A: 4-alpha-glucanotransferase, chloroplastic/amyloplastic
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)121,7796
Polymers118,4472
Non-polymers3,3314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area12990 Å2
ΔGint62 kcal/mol
Surface area42740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.841, 120.413, 174.552
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 4-alpha-glucanotransferase, chloroplastic/amyloplastic / Amylomaltase / Disproportionating enzyme / D-enzyme


Mass: 59223.660 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: Polysaccharide 4-deoxy-alpha-D-glucopyranose-(1-4)-4-deoxy-alpha-D-glucopyranose-(1-4)-4-deoxy-alpha-D- ...4-deoxy-alpha-D-glucopyranose-(1-4)-4-deoxy-alpha-D-glucopyranose-(1-4)-4-deoxy-alpha-D-glucopyranose-(1-4)-4-deoxy-alpha-D-glucopyranose-(1-4)-4-deoxy-alpha-D-glucopyranose-(1-4)-4-deoxy-alpha-D-glucopyranose-(1-4)-4-deoxy-alpha-D-glucopyranose-(1-4)-4-deoxy-alpha-D-glucopyranose-(1-4)-4-deoxy-alpha-D-glucopyranose-(1-4)-4-deoxy-alpha-D-glucopyranose-(1-4)-4-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1625.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,11,10/[a2112h-1a_1-5][a21d2h-1a_1-5]/1-1-1-1-1-1-1-1-1-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1_h4-i1_i4-j1_j4-k1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-4-deoxy-Glcp]{}}}}}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.6
Details: 12% (w/v) 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: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→60.9 Å / Num. obs: 46979 / % possible obs: 99.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.062 / Net I/av σ(I): 17.1 / Net I/σ(I): 5.7
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 6745 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X1N

1x1n


Resolution: 2.05→49.56 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19636 2377 5.1 %RANDOM
Rwork0.16632 ---
obs0.16786 44590 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.199 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.05→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4183 0 122 288 4593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134439
X-RAY DIFFRACTIONr_bond_other_d0.0340.0174029
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.6736025
X-RAY DIFFRACTIONr_angle_other_deg2.3151.6159383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.475524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98722.458240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61915708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9831529
X-RAY DIFFRACTIONr_chiral_restr0.0840.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024859
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02936
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_it2.9363.1122093
X-RAY DIFFRACTIONr_mcbond_other2.9193.112092
X-RAY DIFFRACTIONr_mcangle_it3.824.6492615
X-RAY DIFFRACTIONr_mcangle_other3.8234.652616
X-RAY DIFFRACTIONr_scbond_it4.0773.6512345
X-RAY DIFFRACTIONr_scbond_other4.073.6522345
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9325.2873410
X-RAY DIFFRACTIONr_long_range_B_refined7.17837.6365171
X-RAY DIFFRACTIONr_long_range_B_other7.17237.515121
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 187 -
Rwork0.194 3214 -
obs--98.98 %

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