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- PDB-4hln: Structure of barley starch synthase I in complex with maltooligos... -

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Basic information

Entry
Database: PDB / ID: 4hln
TitleStructure of barley starch synthase I in complex with maltooligosaccharide
ComponentsStarch synthase I
KeywordsTRANSFERASE / Double Rossmann fold / glycosyltransferase / ADPglucose / Maltooligosaccharide / Glycogen / Amylopectin / Disulfide / Plastidial
Function / homology
Function and homology information


endosperm development / amylopectin biosynthetic process / starch synthase activity / starch biosynthetic process / amyloplast / glycogen (starch) synthase activity / Transferases; Glycosyltransferases; Hexosyltransferases / chloroplast stroma
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
alpha-maltopentaose / Starch synthase, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCuesta-Seijo, J.A. / Nielsen, M.M. / Marri, L. / Tanaka, H. / Palcic, M.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of starch synthase I from barley: insight into regulatory mechanisms of starch synthase activity
Authors: Cuesta-Seijo, J.A. / Nielsen, M.M. / Marri, L. / Tanaka, H. / Beeren, S.R. / Palcic, M.M.
History
DepositionOct 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / 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_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Starch synthase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7262
Polymers69,8971
Non-polymers8291
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.150, 153.150, 84.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-813-

HOH

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Components

#1: Protein Starch synthase I


Mass: 69897.125 Da / Num. of mol.: 1 / Fragment: UNP residues 32-643
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Gene: SSI, glgA2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9M5A3, starch synthase (glycosyl-transferring)
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltopentaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 4.11 Å3/Da / Density % sol: 70.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 17% PEG 8000, 0.1M sodium cacodylate, 0.2M ammonium sulfate, sodium chloride, glycerol, ADPglucose, maltotriose, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2010
RadiationMonochromator: Silicon 1 1 1 channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. all: 31831 / Num. obs: 31291 / % possible obs: 98.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 54.16 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.66
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.24 / Num. unique all: 3165 / % possible all: 97.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→24.737 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8656 / SU ML: 0.28 / Isotropic thermal model: isotropic / σ(F): -3 / Phase error: 20.35 / Stereochemistry target values: Phaser
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 939 3 %Random
Rwork0.1731 ---
all0.1739 31289 --
obs0.1739 31289 98.5 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.702 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 175.08 Å2 / Biso mean: 60.6 Å2 / Biso min: 20.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.698 Å2-0 Å2-0 Å2
2--1.698 Å2-0 Å2
3----3.3959 Å2
Refinement stepCycle: LAST / Resolution: 2.7→24.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 55 23 4058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084156
X-RAY DIFFRACTIONf_angle_d1.2725658
X-RAY DIFFRACTIONf_dihedral_angle_d17.6921510
X-RAY DIFFRACTIONf_chiral_restr0.083614
X-RAY DIFFRACTIONf_plane_restr0.005719
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.84230.32251320.2688428198
2.8423-3.02010.23551350.22694357100
3.0201-3.25280.25411340.2028433899
3.2528-3.57930.25071340.1962431899
3.5793-4.09520.22131300.17422596
4.0952-5.15180.12741360.1288437799
5.1518-24.73770.16971380.1582445498
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)
10.12960.1696-0.11950.2509-0.11680.1644-0.0068-0.03450.01780.00590.02920.06350.09220.0265-0.00540.46110.0224-0.01790.12370.00490.1388-4.555125.35835.3712
20.44120.2117-0.07330.4923-0.13130.16870.10670.00990.10770.1229-0.02250.0744-0.1013-0.1047-0.01240.4208-0.16770.03690.18210.02640.2523-29.2398107.420918.2509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 95:369A95 - 369
2X-RAY DIFFRACTION2chain A and resid 370:612A370 - 612

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