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- PDB-5cpt: Disproportionating enzyme 1 from Arabidopsis - beta cyclodextrin soak -

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Basic information

Entry
Database: PDB / ID: 5cpt
TitleDisproportionating enzyme 1 from Arabidopsis - beta cyclodextrin 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


amyloplast / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / : / starch catabolic process / maltose 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 / 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 / _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

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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)128,31820
Polymers126,6402
Non-polymers1,67818
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint41 kcal/mol
Surface area41300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.750, 73.110, 79.330
Angle α, β, γ (deg.)65.440, 69.480, 66.850
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 46-576
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 BL21(DE3) (bacteria) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.76 %
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→70.323 Å / Num. all: 52530 / Num. obs: 52530 / % possible obs: 92.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 41.1 Å2 / Rpim(I) all: 0.044 / Rrim(I) all: 0.1 / Rsym value: 0.081 / Net I/av σ(I): 8.214 / Net I/σ(I): 11.8 / Num. measured all: 276058
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
2.3-2.365.30.6911.12060039010.3720.6912.592.5
2.36-2.425.40.5451.32051438220.2940.545394
2.42-2.495.30.4331.72018037850.2340.4333.794.5
2.49-2.575.30.3791.91920636130.2050.3794.393.6
2.57-2.665.30.3072.41851535010.1670.307593.9
2.66-2.755.30.262.81801534140.1420.265.893.6
2.75-2.855.20.2133.41696232390.1170.2136.792.6
2.85-2.975.30.1694.31623530630.0930.1698.291.7
2.97-3.15.20.135.71500828990.0730.131090.4
3.1-3.255.10.1076.91354326730.060.10711.586.2
3.25-3.4350.0848.71258825220.0470.08414.384.9
3.43-3.645.30.06411.31396126590.0350.06418.196
3.64-3.895.30.05612.41306024820.030.05620.995.5
3.89-4.25.30.04714.31212122990.0250.04723.495.4
4.2-4.65.30.04215.21131521360.0220.04225.895
4.6-5.145.20.04315.3978418820.0220.0432693.4
5.14-5.945.20.04415.2835616060.0230.04425.790
5.94-7.275.20.04115.9660312680.0210.04126.284.5
7.27-10.295.40.02722.1616511390.0140.0273098.4
10.29-70.3235.30.02721.833276270.0150.02732.498.4

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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→63.63 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.1606 / FOM work R set: 0.8712 / SU B: 11.635 / SU ML: 0.137 / SU R Cruickshank DPI: 0.2816 / SU Rfree: 0.1931 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2692 5.1 %RANDOM
Rwork0.1633 ---
obs0.165 49836 92.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.84 Å2 / Biso mean: 40.1 Å2 / Biso min: 19.56 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å21.08 Å20.48 Å2
2---1.3 Å2-0.78 Å2
3---0.2 Å2
Refinement stepCycle: final / Resolution: 2.3→63.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7938 0 108 333 8379
Biso mean--51.62 41.36 -
Num. residues----1025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198273
X-RAY DIFFRACTIONr_bond_other_d0.0030.027585
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.94311243
X-RAY DIFFRACTIONr_angle_other_deg0.882317402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64151023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35723.886368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.774151235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3271546
X-RAY DIFFRACTIONr_chiral_restr0.0730.21207
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219404
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021942
X-RAY DIFFRACTIONr_mcbond_it1.2472.374098
X-RAY DIFFRACTIONr_mcbond_other1.2412.374097
X-RAY DIFFRACTIONr_mcangle_it2.0033.5515116
Refine LS restraints NCS

Ens-ID: 1 / Number: 29726 / 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→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 173 -
Rwork0.244 3720 -
all-3893 -
obs--92.43 %
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)
10.2474-1.1494-0.59597.97712.47315.7684-0.2829-0.011-0.25991.1437-0.07870.96060.6408-0.18720.36160.4051-0.06280.12760.4052-0.07690.79373.681238.023341.0723
21.75120.0889-0.69043.09572.18684.49490.0779-0.005-0.06360.0113-0.08310.18620.14090.04190.00520.0163-0.0003-0.01720.02350.00320.034325.3611.71526.1181
32.22390.63710.22744.0804-0.35133.33910.1050.1974-0.281-0.0687-0.0270.0390.5534-0.1258-0.0780.2038-0.01040.00110.0948-0.01820.048519.9972-11.953414.3544
40.080.1347-0.16920.81981.06096.6205-0.00910.05740.0157-0.1109-0.0350.07490.2238-0.27690.04410.07190.0295-0.02530.08330.02070.085119.1609-3.88833.8464
50.68410.3505-0.02213.31361.33723.8985-0.01830.15830.1096-0.44180.1382-0.139-0.42350.2543-0.120.1629-0.0229-0.02780.10680.03410.070827.169316.60574.6022
61.4117-0.4935-0.26213.581.07451.38950.0571-0.1501-0.05340.18520.0723-0.29240.08390.3005-0.12940.02-0.0038-0.03050.09820.00630.047937.121412.485131.2405
76.30363.76387.09627.99896.77679.1403-0.06570.15230.2086-0.12460.1124-0.285-0.15510.2458-0.04670.5506-0.14080.08510.3485-0.00960.396333.93931.91565.1225
81.3076-0.3512-1.99566.31572.96644.6071-0.0959-0.04750.0586-0.01450.1012-0.2734-0.03270.2507-0.00530.0504-0.0319-0.0490.04370.04430.076140.474551.568843.0601
92.5720.1591-0.10864.2537-0.33712.20270.0506-0.19450.38230.33320.0207-0.288-0.29720.1154-0.07130.0980.0094-0.02020.1157-0.04580.119535.615669.568149.9175
104.1795-3.0736-1.44613.3641.15440.52410.12160.05220.2642-0.1095-0.0515-0.0642-0.0632-0.0576-0.07020.09060.0025-0.03810.1239-0.00070.053823.41571.125446.2227
112.2967-1.1238-0.61884.10781.60691.2041-0.05470.0732-0.28410.113-0.23060.70140.1084-0.32050.28540.07330.0046-0.03180.1493-0.04210.220812.244453.123742.4911
120.7909-0.09780.04173.23611.69392.806-0.1151-0.1583-0.10020.51620.0508-0.16520.30130.10080.06420.11840.0106-0.02590.06130.0470.053734.996936.881448.7114
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 77
2X-RAY DIFFRACTION2A78 - 134
3X-RAY DIFFRACTION3A135 - 214
4X-RAY DIFFRACTION4A215 - 293
5X-RAY DIFFRACTION5A294 - 438
6X-RAY DIFFRACTION6A439 - 576
7X-RAY DIFFRACTION7B60 - 76
8X-RAY DIFFRACTION8B77 - 122
9X-RAY DIFFRACTION9B123 - 212
10X-RAY DIFFRACTION10B213 - 294
11X-RAY DIFFRACTION11B295 - 438
12X-RAY DIFFRACTION12B439 - 576

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