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- PDB-5csu: Disproportionating enzyme 1 from Arabidopsis - acarviostatin soak -

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Basic information

Entry
Database: PDB / ID: 5csu
TitleDisproportionating enzyme 1 from Arabidopsis - acarviostatin 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
5-HYDROXYMETHYL-CHONDURITOL / 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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 / 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_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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)129,15713
Polymers126,6402
Non-polymers2,51611
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint40 kcal/mol
Surface area40600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.830, 74.130, 79.730
Angle α, β, γ (deg.)64.590, 69.760, 66.570
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

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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
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 , 2 types, 4 molecules

#2: Polysaccharide 4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 325.313 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DQuip[4N]a1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122m-1a_1-5_4*N]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{}}LINUCSPDB-CARE
#3: Polysaccharide 4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 487.454 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DQuip[4N]a1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2122h-1a_1-5][a2122m-1a_1-5_4*N]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 207 molecules

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-HMC / 5-HYDROXYMETHYL-CHONDURITOL


Mass: 176.167 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C7H12O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
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: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.53→40.95 Å / Num. obs: 42064 / % possible obs: 95.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 31.5 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.085 / Net I/σ(I): 5.7 / Num. measured all: 123306
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.9 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.53-2.60.5151.9899231040.7010.35896.4
11.31-40.950.06211.612144240.9890.04486.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X1N

1x1n


Resolution: 2.53→40.95 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.2493 / WRfactor Rwork: 0.2058 / FOM work R set: 0.7838 / SU B: 23.106 / SU ML: 0.252 / SU R Cruickshank DPI: 0.6192 / SU Rfree: 0.2977 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.619 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 2181 5.2 %RANDOM
Rwork0.2072 ---
obs0.2094 39812 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.61 Å2 / Biso mean: 42.6 Å2 / Biso min: 19.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20.8 Å20.66 Å2
2---0.31 Å2-1.2 Å2
3---0.63 Å2
Refinement stepCycle: final / Resolution: 2.53→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7992 0 164 200 8356
Biso mean--49.85 40.36 -
Num. residues----1036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198392
X-RAY DIFFRACTIONr_bond_other_d0.0040.027614
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.94311463
X-RAY DIFFRACTIONr_angle_other_deg1.1317495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18451034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20223.781365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.668151232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6071547
X-RAY DIFFRACTIONr_chiral_restr0.0770.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219523
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021968
X-RAY DIFFRACTIONr_mcbond_it0.9162.7774142
X-RAY DIFFRACTIONr_mcbond_other0.912.7764141
X-RAY DIFFRACTIONr_mcangle_it1.5434.1645174
Refine LS restraints NCS

Ens-ID: 1 / Number: 58012 / 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: 2.53→2.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 173 -
Rwork0.276 2895 -
all-3068 -
obs--95.61 %
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)
15.4044-4.2252-0.51559.4360.68153.5141-0.3473-0.2192-0.06810.41070.3810.39490.0599-0.1845-0.03370.2182-0.11530.04270.1985-0.10870.28442.989840.713442.9449
21.1350.81010.57612.581.31153.531-0.02310.1603-0.1404-0.08530.03410.11440.4628-0.1032-0.0110.1855-0.03930.07730.0353-0.03820.12522.6723-4.963719.8409
30.1394-0.2202-0.5670.68481.59826.35330.040.05730.0134-0.0518-0.09340.11420.0944-0.33040.05340.1395-0.02990.06680.0403-0.0160.119119.2663-3.47824.0977
40.90.49190.52661.76580.85882.7720.0740.1211-0.0057-0.21630.02860.0117-0.2854-0.0465-0.10260.2458-0.02910.11340.0403-0.03080.0728.128911.69372.5966
52.535-0.341-1.02552.26310.4913.722-0.0939-0.087-0.1091-0.05480.0840.0503-0.11180.07810.010.232-0.06140.07190.0378-0.04220.096429.607821.2678.9236
61.0616-0.2541-0.63972.75160.73321.6562-0.0284-0.0711-0.0280.10130.0726-0.23310.05770.3054-0.04430.1174-0.04220.07060.0833-0.04020.076637.194913.294231.3106
71.32230.4615-0.77630.73291.2867.78240.0347-0.0796-0.0422-0.22360.2018-0.1797-0.27640.3927-0.23650.362-0.03440.06470.2110.01430.303135.964433.16348.0123
80.9341-0.655-0.16784.4820.40261.50050.0421-0.02840.21230.16650.0143-0.2123-0.14050.0226-0.05640.0965-0.04540.04830.0262-0.03070.072637.516759.179946.7215
91.5848-0.60120.32294.4931-1.20044.4352-0.1426-0.14520.14730.380.107-0.2039-0.3476-0.17030.03560.1336-0.02130.08910.1301-0.10620.181436.889274.247749.8965
104.5523-2.9574-1.69872.71161.15750.92480.08950.11360.1454-0.1158-0.1141-0.0418-0.1633-0.06080.02450.1506-0.03430.03280.0298-0.03770.077323.737172.484646.0259
111.4018-0.2858-0.10522.1980.26361.05070.01410.193-0.1823-0.0622-0.12630.23470.0682-0.1640.11210.1482-0.0420.10630.0825-0.10080.16712.879753.514943.846
121.05240.372-0.19542.56391.061.9034-0.0496-0.1685-0.18240.3223-0.0002-0.0790.11210.09040.04980.1749-0.0240.09640.04150.00060.099134.895138.030448.4377
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A59 - 75
2X-RAY DIFFRACTION2A76 - 212
3X-RAY DIFFRACTION3A213 - 294
4X-RAY DIFFRACTION4A295 - 370
5X-RAY DIFFRACTION5A371 - 438
6X-RAY DIFFRACTION6A439 - 576
7X-RAY DIFFRACTION7B59 - 80
8X-RAY DIFFRACTION8B81 - 162
9X-RAY DIFFRACTION9B163 - 212
10X-RAY DIFFRACTION10B213 - 294
11X-RAY DIFFRACTION11B295 - 437
12X-RAY DIFFRACTION12B438 - 576

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