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- PDB-5csy: Disproportionating enzyme 1 from Arabidopsis - acarbose soak -

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Basic information

Entry
Database: PDB / ID: 5csy
TitleDisproportionating enzyme 1 from Arabidopsis - acarbose 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-maltotriose / 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 23, 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 / Non-polymer description / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _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
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 23, 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)129,62616
Polymers126,6402
Non-polymers2,98614
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11310 Å2
ΔGint39 kcal/mol
Surface area40510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.790, 73.690, 79.350
Angle α, β, γ (deg.)64.590, 69.990, 66.780
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

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Protein , 1 types, 2 molecules AB

#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

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Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-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)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1132.028 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,6,5/[a2122h-1a_1-5][a2122m-1a_1-5]/1-1-2-1-1-1/a4-b1_b4-c1_c4n2-d1n1*1OC^RC^RC^SC^SN*2/6C=^ZCCO/10$3/5O/4O_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][non_ch_ring]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 414 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 52.98 %
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: Sep 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.05→63.67 Å / Num. obs: 72219 / % possible obs: 89.7 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.051 / Net I/σ(I): 14.3 / Num. measured all: 303777 / Scaling rejects: 25
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.05-2.14.11.0191.62093251620.6360.5787
9.17-63.674.30.02662.338688910.9980.01499.1

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Processing

Software
NameVersionClassification
Aimless0.2.13data scaling
REFMAC5.8.0123refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X1N

1x1n


Resolution: 2.05→63.67 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1904 / WRfactor Rwork: 0.1673 / FOM work R set: 0.7956 / SU B: 10.816 / SU ML: 0.139 / SU R Cruickshank DPI: 0.2035 / SU Rfree: 0.1612 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 3689 5.1 %RANDOM
Rwork0.1871 ---
obs0.1883 68519 89.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.65 Å2 / Biso mean: 43.944 Å2 / Biso min: 23.29 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20.29 Å20.8 Å2
2---1.32 Å2-1.2 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.05→63.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7997 0 199 404 8600
Biso mean--55.41 43.29 -
Num. residues----1023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198440
X-RAY DIFFRACTIONr_bond_other_d0.0050.027701
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.94311488
X-RAY DIFFRACTIONr_angle_other_deg1.21317728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24351024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61624.13385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.629151276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0981546
X-RAY DIFFRACTIONr_chiral_restr0.0870.21254
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219490
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021956
X-RAY DIFFRACTIONr_mcbond_it1.0412.5494093
X-RAY DIFFRACTIONr_mcbond_other1.042.5494092
X-RAY DIFFRACTIONr_mcangle_it1.663.8195112
Refine LS restraints NCS

Ens-ID: 1 / Number: 57822 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 259 -
Rwork0.299 4894 -
all-5153 -
obs--86.91 %
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)
14.2603-4.7296-1.78785.89332.32291.01430.0456-0.1622-0.3499-0.0597-0.22710.79730.0458-0.1850.18150.2999-0.04530.02590.2805-0.12930.67775.282536.565540.865
20.95630.65990.25962.88971.14453.6791-0.08970.1887-0.168-0.14030.0983-0.08250.5668-0.0802-0.00860.1786-0.04520.05180.0427-0.03830.052422.1372-6.394318.6077
30.02150.10170.11050.89491.6157.26910.01380.01580.0158-0.0616-0.05220.05550.1226-0.19940.03840.1230.0330.01440.0839-0.01130.052120.612-2.07073.1958
46.14222.38392.26882.7567-0.9222.6781-1.15450.6272-0.5185-0.28870.4436-1.1817-0.72380.29310.71090.7658-0.19770.1590.8345-0.51010.782738.27613.28081.4981
52.17082.17370.91675.24422.27164.7461-0.03290.09060.1786-0.52310.1069-0.0739-0.4135-0.167-0.07390.31360.0109-0.00550.05630.01340.104923.272319.06768.94
61.944-0.0299-0.53023.70330.79171.8029-0.0222-0.0645-0.04440.10880.1344-0.35410.08720.3659-0.11230.0578-0.00480.00070.0933-0.03660.050236.86113.231231.2187
70.3503-0.8258-0.88557.09140.90812.54440.0456-0.08510.1484-0.48380.3399-0.0354-0.00680.2934-0.38550.5155-0.12710.10250.48370.00090.463734.642930.36051.3698
81.6895-0.5748-1.36664.59881.7312.3192-0.08040.06170.0123-0.10920.0387-0.1378-0.07320.04510.04180.0592-0.0151-0.00270.01020.00680.014138.025952.157741.6294
93.97940.7561-0.194.2654-0.39371.5650.1073-0.17460.33510.3302-0.0661-0.2518-0.17290.0994-0.04120.1563-0.01720.02940.0516-0.06110.120335.037271.752648.9059
103.3952-2.6349-1.232.64751.08020.8656-0.02190.0040.0949-0.05210.0020.0378-0.1151-0.12160.01990.10290.0083-0.00150.0503-0.01980.035720.958770.822246.6501
111.4601-1.3942-0.40393.16290.47380.4479-0.06270.0808-0.12610.1741-0.14550.55640.0373-0.21670.20820.153-0.03840.06110.1205-0.11420.187616.67847.343343.9767
121.004-0.2341-0.03043.436512.8727-0.1006-0.169-0.17460.53270.074-0.17370.30310.23730.02660.18430.02570.00910.04890.03240.050737.718939.2449.2607
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 81
2X-RAY DIFFRACTION2A82 - 217
3X-RAY DIFFRACTION3A218 - 311
4X-RAY DIFFRACTION4A312 - 340
5X-RAY DIFFRACTION5A341 - 438
6X-RAY DIFFRACTION6A439 - 576
7X-RAY DIFFRACTION7B60 - 72
8X-RAY DIFFRACTION8B73 - 130
9X-RAY DIFFRACTION9B131 - 217
10X-RAY DIFFRACTION10B218 - 314
11X-RAY DIFFRACTION11B315 - 484
12X-RAY DIFFRACTION12B485 - 576

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