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- PDB-6gne: Catalytic domain of Starch Synthase IV from Arabidopsis thaliana ... -

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Basic information

Entry
Database: PDB / ID: 6gne
TitleCatalytic domain of Starch Synthase IV from Arabidopsis thaliana bound to ADP and acarbose
ComponentsProbable starch synthase 4, chloroplastic/amyloplastic
KeywordsTRANSFERASE / Glycosyl Transferase / Starch Synthase / Acarbose / ADP
Function / homology
Function and homology information


starch synthase (glycosyl-transferring) / alpha-1,4-glucan synthase activity / starch synthase activity / starch biosynthetic process / amyloplast / starch metabolic process / glycogen (starch) synthase activity / chloroplast
Similarity search - Function
Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain
Similarity search - Domain/homology
alpha-maltose / alpha-acarbose / ADENOSINE-5'-DIPHOSPHATE / Probable starch synthase 4, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsCuesta-Seijo, J.A. / Ruzanski, C. / Krucewicz, K. / Striebeck, A. / Palcic, M.M.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Denmark
CitationJournal: Front Plant Sci / Year: 2018
Title: Crystal Structures of theCatalyticDomain ofArabidopsis thalianaStarch Synthase IV, of Granule Bound Starch Synthase From CLg1 and of Granule Bound Starch Synthase I ofCyanophora ...Title: Crystal Structures of theCatalyticDomain ofArabidopsis thalianaStarch Synthase IV, of Granule Bound Starch Synthase From CLg1 and of Granule Bound Starch Synthase I ofCyanophora paradoxaIllustrate Substrate Recognition in Starch Synthases.
Authors: Nielsen, M.M. / Ruzanski, C. / Krucewicz, K. / Striebeck, A. / Cenci, U. / Ball, S.G. / Palcic, M.M. / Cuesta-Seijo, J.A.
History
DepositionMay 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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.mon_nstd_flag / _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 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / 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_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_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: Probable starch synthase 4, chloroplastic/amyloplastic
B: Probable starch synthase 4, chloroplastic/amyloplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0827
Polymers114,5942
Non-polymers2,4885
Water2,072115
1
A: Probable starch synthase 4, chloroplastic/amyloplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7124
Polymers57,2971
Non-polymers1,4153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable starch synthase 4, chloroplastic/amyloplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3703
Polymers57,2971
Non-polymers1,0732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.760, 166.940, 47.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
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: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 23 - 514 / Label seq-ID: 8 - 499

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Probable starch synthase 4, chloroplastic/amyloplastic / AtSS4 / Soluble starch synthase IV / SSIV


Mass: 57296.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SS4, At4g18240, T9A21.90 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0WVX5, starch synthase (glycosyl-transferring)
#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...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 / alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Li2SO4, 0.1 M Bis-tris pH 5.5, 25% PEG3350, ZnCl2, ADP, acarbose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→200 Å / Num. obs: 32689 / % possible obs: 93.6 % / Redundancy: 6.1 % / CC1/2: 0.996 / Rrim(I) all: 0.134 / Net I/σ(I): 11.93
Reflection shellResolution: 2.55→2.7 Å / Redundancy: 2.8 % / Num. unique obs: 4558 / CC1/2: 0.608 / Rrim(I) all: 0.871 / % possible all: 84.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QZS

2qzs


Resolution: 2.55→41.87 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 20.373 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R Free: 0.302 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22609 981 3 %RANDOM
Rwork0.18215 ---
obs0.18347 31707 93.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.961 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å2-0 Å2
2--1.56 Å20 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 2.55→41.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7859 0 165 115 8139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198233
X-RAY DIFFRACTIONr_bond_other_d0.0020.027432
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.96811166
X-RAY DIFFRACTIONr_angle_other_deg0.994317270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4335985
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97423.673392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.085151352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6561552
X-RAY DIFFRACTIONr_chiral_restr0.0910.21219
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219071
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021757
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.312.9443946
X-RAY DIFFRACTIONr_mcbond_other1.312.9433945
X-RAY DIFFRACTIONr_mcangle_it2.2554.4124929
X-RAY DIFFRACTIONr_mcangle_other2.2554.4124930
X-RAY DIFFRACTIONr_scbond_it1.4533.1434287
X-RAY DIFFRACTIONr_scbond_other1.4533.1434287
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.494.6516238
X-RAY DIFFRACTIONr_long_range_B_refined5.49255.48633953
X-RAY DIFFRACTIONr_long_range_B_other5.49255.47833951
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 32142 / 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: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 50 -
Rwork0.36 1635 -
obs--67.02 %
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)
12.8921-0.29050.58711.742-0.23231.3736-0.0732-0.0767-0.05730.17820.0735-0.29690.02160.0705-0.00030.057-0.00350.00920.0187-0.02890.0969-28.890115.0504-11.2553
23.8939-0.64080.54231.24510.03761.2487-0.118-0.1794-0.1013-0.07220.08120.01920.0229-0.02170.03680.06090.01660.02670.02140.01390.0155-90.4725.8808-8.1157
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 515
2X-RAY DIFFRACTION2B23 - 516

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