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- PDB-5cq1: Disproportionating enzyme 1 from Arabidopsis - cycloamylose soak -

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Basic information

Entry
Database: PDB / ID: 5cq1
TitleDisproportionating enzyme 1 from Arabidopsis - cycloamylose soak
Components4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
KeywordsTRANSFERASE / disproportionating enzyme 1 / 4-alpha-glucanotransferase / Glycoside Hydrolase Family 77 / starch degradation
Function / homology
Function and homology information


maltose catabolic process / amyloplast / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / starch catabolic process / chloroplast / glucose metabolic process
Similarity search - Function
Glycoside hydrolase, family 77 / 4-alpha-glucanotransferase / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-maltose / alpha-D-glucopyranose / 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsO'Neill, E.C. / Stevenson, C.E.M. / Tantanarat, K. / Latousakis, D. / Donaldson, M.I. / Rejzek, M. / Limpaseni, T. / Smith, A.M. / Field, R.A. / Lawson, D.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Dissection of the Maltodextrin Disproportionation Cycle of the Arabidopsis Plastidial Disproportionating Enzyme 1 (DPE1).
Authors: O'Neill, E.C. / Stevenson, C.E. / Tantanarat, K. / Latousakis, D. / Donaldson, M.I. / Rejzek, M. / Nepogodiev, S.A. / Limpaseni, T. / Field, R.A. / Lawson, D.M.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
B: 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,49821
Polymers126,6402
Non-polymers1,85819
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9480 Å2
ΔGint48 kcal/mol
Surface area41250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.890, 73.350, 79.390
Angle α, β, γ (deg.)65.280, 69.490, 66.860
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 60 - 576 / Label seq-ID: 48 - 564

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic / Amylomaltase / Disproportionating enzyme / D-enzyme / Protein DISPROPORTIONATING ENZYME 1


Mass: 63320.191 Da / Num. of mol.: 2 / Fragment: UNP residues 44-576
Source method: isolated from a genetically manipulated source
Details: The crystallised protein contained residues 46-576 of the wild-type amino acid sequence preceded by an N-terminal nickel affinity tag
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DPE1, At5g64860, MXK3.9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LV91, 4-alpha-glucanotransferase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 microliter of 9% PEG2000 MME in 0.1 M HEPES-NaOH, pH 8.0 was added to 1 microliter of protein at a concentration of 10 mg/ml in 20 mM HEPES-NaOH, pH 7.5, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.3→32.028 Å / Num. all: 52739 / Num. obs: 52739 / % possible obs: 92.4 % / Redundancy: 5.3 % / Biso Wilson estimate: 41 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.085 / Rsym value: 0.077 / Net I/av σ(I): 8.273 / Net I/σ(I): 14.3 / Num. measured all: 279175
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.365.30.5521.42050939000.2640.552392.2
2.36-2.425.40.4111.82079638560.1930.4113.894.3
2.42-2.495.40.3462.22050838050.1630.3464.594.2
2.49-2.575.40.2992.51960836490.1410.2995.394.1
2.57-2.665.40.25331889135090.1190.2536.193.5
2.66-2.755.30.2123.51827234180.10.2127.293.3
2.75-2.855.30.1824.11736532520.0860.1828.392.8
2.85-2.975.40.1485.11648430640.070.14810.191.7
2.97-3.15.20.1166.51545529490.0560.11612.490.4
3.1-3.255.20.17.41386426830.0480.114.486.5
3.25-3.435.10.0789.31270725020.0380.07817.484.3
3.43-3.645.30.06111.21415826810.0290.06122.396.1
3.64-3.895.30.05412.81329625230.0260.05425.595.9
3.89-4.25.30.04814.11207422880.0230.04828.794.7
4.2-4.65.30.042151130121360.020.04231.294.6
4.6-5.145.20.04214.2967118740.020.04231.693
5.14-5.945.10.04415.3827016130.0210.04430.690
5.94-7.275.20.04214.9660412810.0210.04231.484.3
7.27-10.295.40.03119.8614711440.0140.03136.198.5
10.29-32.0285.20.0292131956120.0140.02939.295.6

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X1N

1x1n


Resolution: 2.3→32.028 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1995 / WRfactor Rwork: 0.1711 / FOM work R set: 0.8496 / SU B: 12.442 / SU ML: 0.148 / SU R Cruickshank DPI: 0.3027 / SU Rfree: 0.2021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 2688 5.1 %RANDOM
Rwork0.1758 ---
obs0.1772 50050 92.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.22 Å2 / Biso mean: 41.1 Å2 / Biso min: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å21.35 Å21.22 Å2
2---1.32 Å2-1.68 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 2.3→32.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7968 0 120 309 8397
Biso mean--59.71 38.92 -
Num. residues----1025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198329
X-RAY DIFFRACTIONr_bond_other_d0.0040.027643
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.94311316
X-RAY DIFFRACTIONr_angle_other_deg0.918317557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94151025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85323.941373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.394151258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.181546
X-RAY DIFFRACTIONr_chiral_restr0.0770.21213
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219437
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021949
X-RAY DIFFRACTIONr_mcbond_it1.1792.1664100
X-RAY DIFFRACTIONr_mcbond_other1.1752.1654099
X-RAY DIFFRACTIONr_mcangle_it1.8963.2445119
Refine LS restraints NCS

Ens-ID: 1 / Number: 29671 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 174 -
Rwork0.25 3708 -
all-3882 -
obs--92.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.385-2.39251.3316.09810.53715.5216-0.437-0.1218-0.29821.30240.14651.09080.5631-0.31830.29050.3702-0.12680.19690.4432-0.08050.95354.630736.630240.3548
21.14370.67290.06042.62021.04673.5699-0.03760.1521-0.1851-0.10980.01320.07130.5777-0.04930.02450.12990.0045-0.00390.09330.01170.070522.5783-6.662519.2874
30.2404-0.0057-0.0521.12340.85824.315-0.02750.12350.0734-0.23110.0347-0.0419-0.10850.1315-0.00720.08280.0249-0.02040.14090.02470.081923.48941.58861.9913
41.63131.2348-0.21993.45120.36763.9789-0.08030.24510.1438-0.4460.11510.0599-0.44020.0518-0.03480.20540.0179-0.05940.16070.04210.076225.020219.11647.444
51.0128-0.5367-0.33213.97620.85991.36760.0587-0.01080.0339-0.01410.1352-0.5053-0.04010.4231-0.19390.0054-0.0157-0.00370.1813-0.02160.093539.030114.147229.0825
61.5449-2.2401-1.633612.99190.8672.3568-0.0452-0.2359-0.22030.6547-0.02710.19970.20610.30150.07230.1907-0.0149-0.11310.16870.03010.115628.75156.787740.4869
70.81990.80912.04891.71863.71388.27710.06810.1135-0.0407-0.48110.1438-0.0913-0.71450.2876-0.21190.6765-0.13020.05050.42360.06670.368833.839133.82248.3919
81.7109-0.3204-0.57894.66220.82431.09220.0677-0.20540.3510.46120.0608-0.2258-0.16980.0928-0.12850.114-0.0188-0.010.12860.00190.09737.381464.148848.1096
95.0328-3.7064-1.66543.52911.340.63150.1298-0.01850.2857-0.1689-0.0564-0.085-0.0959-0.0832-0.07340.0910.0064-0.02560.1550.00010.051523.478271.474946.1621
101.4328-0.9717-0.28645.85512.36571.841-0.09950.0685-0.1840.4536-0.21140.90720.2202-0.40550.31090.11690.0021-0.00740.2124-0.03040.307611.660157.080544.8074
111.9082-2.4520.17245.91530.67850.332-0.1383-0.14260.02520.2418-0.1370.75320.0018-0.19580.27530.0829-0.0034-0.00450.2925-0.09060.247416.937741.950940.4197
121.0532-0.0511-0.08863.94341.04983.0157-0.0475-0.2002-0.09250.59790.0534-0.14350.29140.1551-0.00590.10540.004-0.03420.09170.06110.056136.802738.223149.4341
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 79
2X-RAY DIFFRACTION2A80 - 213
3X-RAY DIFFRACTION3A214 - 343
4X-RAY DIFFRACTION4A344 - 436
5X-RAY DIFFRACTION5A437 - 551
6X-RAY DIFFRACTION6A552 - 576
7X-RAY DIFFRACTION7B60 - 80
8X-RAY DIFFRACTION8B81 - 212
9X-RAY DIFFRACTION9B213 - 294
10X-RAY DIFFRACTION10B295 - 386
11X-RAY DIFFRACTION11B387 - 461
12X-RAY DIFFRACTION12B462 - 576

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