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- PDB-6gng: Granule Bound Starch Synthase I from Cyanophora paradoxa bound to... -

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Basic information

Entry
Database: PDB / ID: 6gng
TitleGranule Bound Starch Synthase I from Cyanophora paradoxa bound to acarbose and ADP
ComponentsGranule-bound starch synthase
KeywordsTRANSFERASE / Glycosyl Transferase / Starch Synthase / Acarbose / ADP
Function / homology
Function and homology information


alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / nucleotide binding
Similarity search - Function
Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-acarbose / ADENOSINE-5'-DIPHOSPHATE / Granule-bound starch synthase
Similarity search - Component
Biological speciesCyanophora paradoxa (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsCuesta-Seijo, J.A. / Nielsen, M.M. / 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: 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.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _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: Granule-bound starch synthase
B: Granule-bound starch synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,9116
Polymers132,7662
Non-polymers2,1464
Water724
1
A: Granule-bound starch synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4563
Polymers66,3831
Non-polymers1,0732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Granule-bound starch synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4563
Polymers66,3831
Non-polymers1,0732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.300, 106.100, 175.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 18 - 541 / Label seq-ID: 38 - 561

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

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Components

#1: Protein Granule-bound starch synthase


Mass: 66382.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanophora paradoxa (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: A8V967
#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)-beta-D-glucopyranose / beta-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: beta-acarbose
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/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]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 40 mM citric acid, 60 mM bis-tris propane pH 6.4 and 20% PEG 3350, 0.025 M chromium chloride, acarbose, ADP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.9→200 Å / Num. obs: 26755 / % possible obs: 90.8 % / Redundancy: 3.5 % / CC1/2: 0.968 / Rrim(I) all: 0.371 / Net I/σ(I): 4.59
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.72 / Num. unique obs: 2584 / CC1/2: 0.429 / Rrim(I) all: 2.49 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3vue, 2qzs

3vue

2qzs


Resolution: 2.95→20 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.858 / SU B: 45.589 / SU ML: 0.707 / Cross valid method: THROUGHOUT / ESU R Free: 0.541 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30293 760 3 %RANDOM
Rwork0.27248 ---
obs0.27344 24587 90.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.378 Å2
Baniso -1Baniso -2Baniso -3
1--5.18 Å20 Å20 Å2
2--11.62 Å2-0 Å2
3----6.44 Å2
Refinement stepCycle: 1 / Resolution: 2.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8107 0 142 4 8253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198465
X-RAY DIFFRACTIONr_bond_other_d0.0020.027929
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.98911481
X-RAY DIFFRACTIONr_angle_other_deg1.008318456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28951049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04924.061330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.611151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4081536
X-RAY DIFFRACTIONr_chiral_restr0.0910.21265
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219239
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021693
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_it2.3316.2684202
X-RAY DIFFRACTIONr_mcbond_other2.3316.2684201
X-RAY DIFFRACTIONr_mcangle_it3.9849.3995249
X-RAY DIFFRACTIONr_mcangle_other3.9849.3995250
X-RAY DIFFRACTIONr_scbond_it2.0116.3984263
X-RAY DIFFRACTIONr_scbond_other2.0116.3984264
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5329.5176233
X-RAY DIFFRACTIONr_long_range_B_refined8.8229999.999933723
X-RAY DIFFRACTIONr_long_range_B_other8.8229999.999933724
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 32184 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.95→3.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 56 -
Rwork0.439 1805 -
obs--93.14 %

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