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- PDB-5cpq: Disproportionating enzyme 1 from Arabidopsis - apo form -

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Basic information

Entry
Database: PDB / ID: 5cpq
TitleDisproportionating enzyme 1 from Arabidopsis - apo form
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: 2.13 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 1.3Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)127,50916
Polymers126,6402
Non-polymers86914
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint19 kcal/mol
Surface area42090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.650, 74.220, 79.700
Angle α, β, γ (deg.)64.970, 69.480, 66.020
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: ILE / Beg label comp-ID: ILE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 59 - 576 / Label seq-ID: 47 - 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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
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 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.126→70.515 Å / Num. all: 68185 / Num. obs: 68185 / % possible obs: 92.6 % / Redundancy: 2.7 % / Biso Wilson estimate: 35.7 Å2 / Rpim(I) all: 0.063 / Rrim(I) all: 0.106 / Rsym value: 0.084 / Net I/av σ(I): 4.821 / Net I/σ(I): 6.7 / Num. measured all: 181754
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
2.13-2.242.60.5411.42398490660.4040.5411.784.4
2.24-2.382.70.3542.12594496790.2650.3542.594.8
2.38-2.542.70.2363.12435190920.1760.2363.595
2.54-2.742.70.1624.52262984280.1210.1624.994.8
2.74-3.012.70.116.42073577540.0830.116.794.9
3.01-3.362.70.0787.81865670300.0590.0789.494.5
3.36-3.882.70.0628.91623061160.0470.06212.194.1
3.88-4.752.60.0617.11349351120.0470.06113.692.8
4.75-6.722.60.0645.8957236500.0480.06413.685.6
6.72-57.3952.70.03911.7616022580.0290.0391596.6

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
REFMAC5.8.073refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X1N

1x1n


Resolution: 2.13→57.78 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2264 / WRfactor Rwork: 0.1916 / FOM work R set: 0.824 / SU B: 11.625 / SU ML: 0.15 / SU R Cruickshank DPI: 0.2225 / SU Rfree: 0.1773 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 3459 5.1 %RANDOM
Rwork0.1868 ---
obs0.1884 64404 92.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.69 Å2 / Biso mean: 42.1 Å2 / Biso min: 17.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å21.68 Å20.43 Å2
2---0.51 Å2-1.64 Å2
3---0.24 Å2
Refinement stepCycle: final / Resolution: 2.13→57.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8009 0 64 535 8608
Biso mean--51.94 42.36 -
Num. residues----1026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198281
X-RAY DIFFRACTIONr_bond_other_d0.0040.027603
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.94411251
X-RAY DIFFRACTIONr_angle_other_deg0.934317465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86851022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25624.151383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.326151266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9451546
X-RAY DIFFRACTIONr_chiral_restr0.0750.21191
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219470
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021948
X-RAY DIFFRACTIONr_mcbond_it1.2192.1574100
X-RAY DIFFRACTIONr_mcbond_other1.2162.1574099
X-RAY DIFFRACTIONr_mcangle_it1.9443.2295118
Refine LS restraints NCS

Ens-ID: 1 / Number: 29652 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 200 -
Rwork0.309 3913 -
all-4113 -
obs--76.63 %
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)
12.6726-2.9337-1.12897.38932.95072.0092-0.1455-0.0129-0.0970.2928-0.29170.50630.1696-0.16530.43710.2279-0.04770.02440.4299-0.03560.57074.883537.935140.0798
21.3359-0.0732-0.13882.19570.47733.2570.07680.1426-0.2729-0.2029-0.16690.17130.4720.05310.09010.1320.0013-0.05610.09480.01280.109524.7374-2.091123.3316
35.7575-0.18922.0533.5928-0.12123.76310.21230.0259-0.4918-0.2236-0.0960.30080.7359-0.2028-0.11630.5555-0.0128-0.03010.1739-0.04850.173321.7763-14.296214.9863
40.07310.11340.14321.29961.09643.66210.01040.1198-0.0049-0.3367-0.05580.05680.06890.04090.04540.27360.0801-0.09380.2502-0.0030.166522.08523.8463.403
50.90220.2451.34681.96340.9864.31230.09670.3597-0.0064-0.577-0.0373-0.05-0.22160.3502-0.05940.26580.04490.00630.21770.04040.07730.707422.722513.1371
61.6816-0.8233-0.27823.36321.01041.6830.0737-0.0868-0.0528-0.00380.0065-0.30020.15710.398-0.08030.0624-0.0022-0.03690.1650.04340.062937.180610.831432.5866
70.02380.14970.41453.23024.33728.8677-0.00410.01540.0304-0.58730.0094-0.2331-0.76360.1773-0.00530.5246-0.07540.06610.5260.0720.366334.176833.33637.5894
80.60230.177-0.15144.44890.68921.70340.019-0.20560.03480.24560.0502-0.3833-0.15050.1865-0.06930.0479-0.0373-0.04970.12560.03380.106839.422959.62648.0529
92.1677-0.8731-0.53856.8592-1.78965.84020.0219-0.07140.25560.3990.0672-0.2889-0.505-0.1273-0.08910.0738-0.0353-0.02550.1567-0.03890.217637.457174.152249.7411
107.2417-0.8198-2.12173.61050.45911.60260.014-0.24880.51930.0579-0.06580.1028-0.2729-0.1050.05180.10390.0287-0.10440.1772-0.06110.206517.146877.457549.7623
111.8547-0.01420.30472.99460.90260.8481-0.05-0.029-0.0444-0.0511-0.14290.5304-0.0001-0.22690.19280.0426-0.0109-0.04870.13450.00220.161817.746956.171642.3213
121.17250.17990.28783.48481.39482.5149-0.0566-0.17-0.09320.503-0.0399-0.19290.26910.08830.09650.0872-0.003-0.02850.07770.07010.076935.471537.51748.9559
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A59 - 79
2X-RAY DIFFRACTION2A80 - 163
3X-RAY DIFFRACTION3A164 - 209
4X-RAY DIFFRACTION4A210 - 373
5X-RAY DIFFRACTION5A374 - 461
6X-RAY DIFFRACTION6A462 - 576
7X-RAY DIFFRACTION7B59 - 80
8X-RAY DIFFRACTION8B81 - 169
9X-RAY DIFFRACTION9B170 - 209
10X-RAY DIFFRACTION10B210 - 263
11X-RAY DIFFRACTION11B264 - 438
12X-RAY DIFFRACTION12B439 - 576

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