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- PDB-3vuf: Crystal Structure of Rice Granule bound Starch Synthase I Catalyt... -

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Basic information

Entry
Database: PDB / ID: 3vuf
TitleCrystal Structure of Rice Granule bound Starch Synthase I Catalytic Domain in Complex with ADP
ComponentsGranule-bound starch synthase 1, chloroplastic/amyloplastic
KeywordsTRANSFERASE / Rossmann fold / glycosyltransferase
Function / homology
Function and homology information


NDP-glucose-starch glucosyltransferase / starch biosynthetic process / amyloplast / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / IgE binding / chloroplast / ADP binding
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
ADENOSINE-5'-DIPHOSPHATE / Granule-bound starch synthase 1, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMomma, M. / Fujimoto, Z.
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2012
Title: Interdomain Disulfide Bridge in the Rice Granule Bound Starch Synthase I Catalytic Domain as Elucidated by X-Ray Structure Analysis
Authors: Momma, M. / Fujimoto, Z.
History
DepositionJun 28, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Granule-bound starch synthase 1, chloroplastic/amyloplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0695
Polymers59,3541
Non-polymers7154
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)153.368, 153.368, 153.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

#1: Protein Granule-bound starch synthase 1, chloroplastic/amyloplastic / GBSS-I


Mass: 59354.000 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 83-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Strain: japonica cultivar-group
Gene: WAXY, WX, WX-B, Os06g0133000, LOC_Os06g04200, 134P10.7, P0679C08.19
Plasmid: pET45b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) gold
References: UniProt: Q0DEV5, NDP-glucose-starch glucosyltransferase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.5M Lithium Sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 12909 / % possible obs: 99.8 % / Redundancy: 14 % / Biso Wilson estimate: 93.3 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1254 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VUE

3vue


Resolution: 3→35.19 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.901 / SU B: 17.379 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27088 622 4.9 %RANDOM
Rwork0.22128 ---
obs0.22357 12161 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.855 Å2
Refinement stepCycle: LAST / Resolution: 3→35.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 42 10 3864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223938
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9755336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3925486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07823.988173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.43115672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5111525
X-RAY DIFFRACTIONr_chiral_restr0.1020.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212965
X-RAY DIFFRACTIONr_mcbond_it1.0611.52423
X-RAY DIFFRACTIONr_mcangle_it1.83723895
X-RAY DIFFRACTIONr_scbond_it1.95431515
X-RAY DIFFRACTIONr_scangle_it3.4044.51441
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 56 -
Rwork0.295 844 -
obs--97.72 %

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