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- PDB-5cps: Disproportionating enzyme 1 from Arabidopsis - maltotriose soak -

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Basic information

Entry
Database: PDB / ID: 5cps
TitleDisproportionating enzyme 1 from Arabidopsis - maltotriose 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
4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / 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_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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _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)130,42620
Polymers126,6402
Non-polymers3,78618
Water12,376687
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14160 Å2
ΔGint84 kcal/mol
Surface area40740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.410, 73.130, 79.120
Angle α, β, γ (deg.)65.460, 69.480, 67.090
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 44-756
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)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1477.282 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,9,8/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1_h4-i1WURCSPDB2Glycan 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]{}}}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1315.142 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,8,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 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]{}}}}}}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
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: 1.8→63.745 Å / Num. all: 105329 / Num. obs: 105329 / % possible obs: 89.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 27.2 Å2 / Rpim(I) all: 0.02 / Rrim(I) all: 0.041 / Rsym value: 0.036 / Net I/av σ(I): 15.333 / Net I/σ(I): 20.5 / Num. measured all: 447034
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
1.8-1.854.30.4361.72990669560.2380.436379.9
1.85-1.94.30.3342.33153072880.1810.3343.986.2
1.9-1.954.30.25333161173390.1380.2535.188.9
1.95-2.014.30.1973.93150273320.1070.1976.591.2
2.01-2.084.30.1564.93066571330.0850.156891.1
2.08-2.154.30.1166.62886067340.0630.11610.589.7
2.15-2.234.20.17.62669263230.0550.112.387.4
2.23-2.324.10.089.42416758300.0450.0814.983.4
2.32-2.434.30.06511.42687862720.0360.0651894
2.43-2.554.30.05513.52556360050.030.05521.193.8
2.55-2.684.30.04715.32415356770.0260.04724.493.4
2.68-2.854.20.04117.82263453630.0230.0412892.9
2.85-3.044.20.03520.22084349620.0190.03532.791.2
3.04-3.294.10.03122.11719142120.0180.03137.583.6
3.29-3.64.20.02626.31765042330.0150.0264492
3.6-4.024.20.02329.71668139540.0130.02348.995.2
4.02-4.654.20.0232.21464534990.0110.0251.294
4.65-5.694.10.02131.41171028290.0120.02151.391.1
5.69-8.054.20.02131.2866820870.0120.02151.387
8.05-63.7454.20.01733.8548513010.010.0175698.5

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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: 1.8→63.74 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.1823 / WRfactor Rwork: 0.1563 / FOM work R set: 0.8862 / SU B: 4.314 / SU ML: 0.067 / SU R Cruickshank DPI: 0.1095 / SU Rfree: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1786 5261 5 %RANDOM
Rwork0.1532 ---
obs0.1545 100068 89.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.49 Å2 / Biso mean: 32.2 Å2 / Biso min: 15.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20.26 Å20.46 Å2
2---0.9 Å2-0.27 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.8→63.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8046 0 269 688 9003
Biso mean--42.48 39.58 -
Num. residues----1029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198573
X-RAY DIFFRACTIONr_bond_other_d0.0040.027878
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.94511670
X-RAY DIFFRACTIONr_angle_other_deg0.993318140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7751036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55824.167384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.663151297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8611545
X-RAY DIFFRACTIONr_chiral_restr0.0840.21288
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219541
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021960
X-RAY DIFFRACTIONr_mcbond_it1.2281.8244123
X-RAY DIFFRACTIONr_mcbond_other1.2181.8234122
X-RAY DIFFRACTIONr_mcangle_it1.8372.735151
Refine LS restraints NCS

Ens-ID: 1 / Number: 30119 / 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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 351 -
Rwork0.223 6600 -
all-6951 -
obs--79.92 %
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)
11.1955-2.236-1.03416.23191.5992.6608-0.22460.1043-0.33560.6428-0.1730.77540.4158-0.16380.39760.2808-0.0586-0.00270.3332-0.05440.62444.223636.453240.0774
21.26530.72230.26371.98980.96882.695-0.00110.0677-0.1830.06390.0459-0.12150.44280.1007-0.04480.07920.01720.00010.0099-0.00920.026825.3642-4.284122.5135
35.9716-0.80151.50614.39690.35223.79620.120.2822-0.2595-0.14510.01760.20830.4465-0.1797-0.13760.2304-0.0420.01050.0632-0.01110.028716.6751-14.190511.6519
40.06220.13110.16590.39740.49914.2883-0.01740.03870.0178-0.0780.00970.09720.0555-0.10.00770.06740.023-0.00270.074-0.01180.056819.91-1.23192.8051
51.49810.7282-0.67422.29780.21243.299-0.04390.16870.1098-0.26110.0835-0.0322-0.31530.1435-0.03960.1377-0.0013-0.02250.07110.01180.041127.308518.39536.0149
61.2235-0.338-0.04922.53230.86131.66160.0051-0.0638-0.0260.09450.0865-0.20530.0360.3115-0.09150.00450.006-0.01030.0825-0.02130.028837.066112.535931.0819
74.12491.9022.1934.48214.96589.5448-0.07940.14050.4264-0.29980.1178-0.0515-0.50860.5091-0.03840.3669-0.04350.02580.19170.07290.265433.616531.97644.679
81.6204-0.2377-0.46773.73410.50551.13770.0083-0.1940.14210.24580.0361-0.2124-0.09570.1241-0.04430.0440.0069-0.01190.0501-0.01240.023438.12658.31247.59
91.9787-0.66760.59874.7444-1.9296.67890.0391-0.01290.3110.1650.0714-0.1152-0.3695-0.0563-0.11060.0260.00170.02560.0765-0.06340.143235.172575.72847.4823
103.5929-2.6705-1.26372.38690.89130.4780.08440.01350.1769-0.105-0.0209-0.0294-0.0656-0.0335-0.06360.08340.0196-0.01510.0675-0.02610.043523.16871.291145.9708
112.0057-0.7189-0.34683.1881.06680.881-0.03180.0659-0.29280.06-0.12480.56240.034-0.22820.15660.05350.033-0.01150.1033-0.03590.193711.81153.145742.6423
120.75140.0670.13942.8141.25662.2436-0.0743-0.1496-0.12190.41950.032-0.01250.21970.08450.04230.09210.0340.01170.04080.02710.024434.71336.837948.6914
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 79
2X-RAY DIFFRACTION2A80 - 175
3X-RAY DIFFRACTION3A176 - 209
4X-RAY DIFFRACTION4A210 - 314
5X-RAY DIFFRACTION5A315 - 438
6X-RAY DIFFRACTION6A439 - 576
7X-RAY DIFFRACTION7B60 - 76
8X-RAY DIFFRACTION8B77 - 175
9X-RAY DIFFRACTION9B176 - 210
10X-RAY DIFFRACTION10B211 - 294
11X-RAY DIFFRACTION11B295 - 438
12X-RAY DIFFRACTION12B439 - 576

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