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- PDB-6gnf: Granule Bound Starch Synthase from Cyanobacterium sp. CLg1 bound ... -

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Basic information

Entry
Database: PDB / ID: 6gnf
TitleGranule Bound Starch Synthase from Cyanobacterium sp. CLg1 bound to acarbose and ADP
ComponentsGlycogen synthase
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 / glycogen (starch) synthase activity / glycogen biosynthetic process
Similarity search - Function
Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-acarbose / ADENOSINE-5'-DIPHOSPHATE / alpha-D-glucopyranose / Glycogen synthase
Similarity search - Component
Biological speciesCyanobacterium sp. CLg1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / pdbx_struct_mod_residue / 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.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 / _pdbx_struct_mod_residue.label_asym_id / _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: Glycogen synthase
B: Glycogen synthase
C: Glycogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,26918
Polymers180,6523
Non-polymers3,61815
Water5,477304
1
A: Glycogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6747
Polymers60,2171
Non-polymers1,4576
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0175
Polymers60,2171
Non-polymers7994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5786
Polymers60,2171
Non-polymers1,3615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)194.260, 132.650, 123.690
Angle α, β, γ (deg.)90.00, 126.30, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISAA0 - 52120 - 541
21HISHISBB0 - 52120 - 541
12HISHISAA0 - 52120 - 541
22HISHISCC0 - 52120 - 541
13LEULEUBB-6 - 52114 - 541
23LEULEUCC-6 - 52114 - 541

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Glycogen synthase / / Starch [bacterial glycogen] synthase


Mass: 60217.238 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanobacterium sp. CLg1 (bacteria) / Gene: glgA / Production host: Escherichia coli (E. coli)
References: UniProt: V5SNJ5, starch synthase (glycosyl-transferring)

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Sugars , 2 types, 3 molecules

#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
#5: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 316 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 3.55 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2M (NH4)2SO4, 2% PEG400 and 150 mM Hepes buffer at pH 7.5, acarbose, ADP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.953 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.2→200 Å / Num. obs: 121565 / % possible obs: 94.7 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rrim(I) all: 0.083 / Net I/σ(I): 14.03
Reflection shellResolution: 2.2→2.4 Å / Redundancy: 4.1 % / Num. unique obs: 23165 / CC1/2: 0.48 / Rrim(I) all: 1.47 / % possible all: 78.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VUE

3vue


Resolution: 2.2→48.56 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 13.916 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.164 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22377 3647 3 %RANDOM
Rwork0.20466 ---
obs0.20523 117917 95.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.286 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å2-0 Å20.03 Å2
2--2.29 Å20 Å2
3----0.63 Å2
Refinement stepCycle: 1 / Resolution: 2.2→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11885 0 226 304 12415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01912455
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211879
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.99416945
X-RAY DIFFRACTIONr_angle_other_deg0.792327474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66851528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30725.179504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9152091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7321532
X-RAY DIFFRACTIONr_chiral_restr0.0620.21913
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113792
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022690
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_it1.7954.0676112
X-RAY DIFFRACTIONr_mcbond_other1.7954.0676111
X-RAY DIFFRACTIONr_mcangle_it3.0076.0957631
X-RAY DIFFRACTIONr_mcangle_other3.0076.0967632
X-RAY DIFFRACTIONr_scbond_it2.1424.4096343
X-RAY DIFFRACTIONr_scbond_other2.0974.3736307
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4246.4819258
X-RAY DIFFRACTIONr_long_range_B_refined6.85533.29613873
X-RAY DIFFRACTIONr_long_range_B_other6.71133.14513801
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A592140.07
12B592140.07
21A626550.05
22C626550.05
31B600070.06
32C600070.06
LS refinement shellResolution: 2.204→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.584 193 -
Rwork0.579 6264 -
obs--68.65 %
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)
12.32720.8587-0.75721.4092-1.02522.2-0.0194-0.1344-0.08930.26010.08390.12380.0075-0.4509-0.06450.1348-0.0657-0.00530.25080.06850.1448-33.51171.3209-24.1836
23.5412-1.21863.32512.7935-2.40174.57790.0572-0.7558-0.5661-0.43650.73560.38080.386-1.1321-0.79280.1076-0.0877-0.0140.45170.31190.2745-48.358341.9398-66.5537
31.1964-0.2178-0.72631.79390.65822.10490.245-0.29480.20050.1350.0592-0.0952-0.33590.2035-0.30420.156-0.08250.10520.16390.00590.160314.313330.5241-28.4482
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 521
2X-RAY DIFFRACTION2B-6 - 521
3X-RAY DIFFRACTION3C-8 - 522

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