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- PDB-6lx1: Potato D-enzyme complexed with Acarbose -

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Basic information

Entry
Database: PDB / ID: 6lx1
TitlePotato D-enzyme complexed with Acarbose
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: 2.03 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)59,9406
Polymers59,2241
Non-polymers7165
Water8,197455
1
A: 4-alpha-glucanotransferase, chloroplastic/amyloplastic
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)119,87912
Polymers118,4472
Non-polymers1,43210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7220 Å2
ΔGint-47 kcal/mol
Surface area43640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.171, 120.293, 174.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-604-

MG

21A-1082-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-1,5-anhydro-D-glucitol


Type: oligosaccharide / Mass: 467.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[h2122h_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 459 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.6 / 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: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: Bruker DIP-6040 / Detector: IMAGE PLATE / Date: Apr 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→60 Å / Num. obs: 46983 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 32.3
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 7.9 / Num. unique obs: 4620 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1x1n


Resolution: 2.03→59.96 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20563 2414 5.1 %RANDOM
Rwork0.16331 ---
obs0.16542 44986 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.404 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.03→59.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 46 455 4621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134281
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173913
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.6475814
X-RAY DIFFRACTIONr_angle_other_deg2.3341.5879095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4385512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31722.446233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87115696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4341528
X-RAY DIFFRACTIONr_chiral_restr0.0930.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024763
X-RAY DIFFRACTIONr_gen_planes_other0.0270.02919
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_it3.1433.0922057
X-RAY DIFFRACTIONr_mcbond_other3.1333.0912056
X-RAY DIFFRACTIONr_mcangle_it4.1014.622566
X-RAY DIFFRACTIONr_mcangle_other4.1064.622567
X-RAY DIFFRACTIONr_scbond_it4.3393.5872223
X-RAY DIFFRACTIONr_scbond_other4.3383.5882224
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5315.1843249
X-RAY DIFFRACTIONr_long_range_B_refined7.98537.7135133
X-RAY DIFFRACTIONr_long_range_B_other7.87837.0964999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 190 -
Rwork0.198 3248 -
obs--99.71 %

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