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- PDB-5avg: The 0.95 angstrom structure of thaumatin crystallized in high-str... -

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Basic information

Entry
Database: PDB / ID: 5avg
TitleThe 0.95 angstrom structure of thaumatin crystallized in high-strength agarose hydrogel
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / thaumatin / high-strength agarose / hydrogel
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin / Thaumatin / Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsSugiyama, S. / Shimizu, N. / Maruyama, M. / Sazaki, G. / Hirose, M. / Adachi, H. / Takano, K. / Murakami, S. / Inoue, T. / Mori, Y. / Matsumura, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS KAKENHI23860028 Japan
JSPS KAKENHI25650051 Japan
JSPS KAKENHI25286051 Japan
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Growth of protein crystals in hydrogels prevents osmotic shock
Authors: Sugiyama, S. / Maruyama, M. / Sazaki, G. / Hirose, M. / Adachi, H. / Takano, K. / Murakami, S. / Inoue, T. / Mori, Y. / Matsumura, H.
History
DepositionJun 16, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_nat ...diffrn_source / entity_src_nat / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Thaumatin-1


Theoretical massNumber of molelcules
Total (without water)22,1561
Polymers22,1561
Non-polymers00
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9480 Å2
Unit cell
Length a, b, c (Å)57.839, 57.839, 149.552
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-556-

HOH

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Components

#1: Protein Thaumatin-1 / Thaumatin I


Mass: 22155.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7 / Details: 0.1 M Hepes-NaOH (pH 7.0), 0.33 M Na/K tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.95→53.95 Å / Num. obs: 148780 / % possible obs: 92.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 21.5
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.25 / % possible all: 56

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VHK

2vhk


Resolution: 0.95→53.95 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.386 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14402 7455 5 %RANDOM
Rwork0.12695 ---
obs0.1278 141256 92.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.695 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0 Å2
2--0.24 Å2-0 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 0.95→53.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 0 274 1820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021807
X-RAY DIFFRACTIONr_bond_other_d0.0030.021622
X-RAY DIFFRACTIONr_angle_refined_deg2.2211.9522485
X-RAY DIFFRACTIONr_angle_other_deg1.02433777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0985253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.40623.20578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9515282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1391515
X-RAY DIFFRACTIONr_chiral_restr0.1540.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212159
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02432
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_it1.3591.08927
X-RAY DIFFRACTIONr_mcbond_other1.3591.082928
X-RAY DIFFRACTIONr_mcangle_it1.6931.6321176
X-RAY DIFFRACTIONr_mcangle_other1.591.6311176
X-RAY DIFFRACTIONr_scbond_it2.2421.319880
X-RAY DIFFRACTIONr_scbond_other2.2411.321881
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2981.8731297
X-RAY DIFFRACTIONr_long_range_B_refined3.18210.7832266
X-RAY DIFFRACTIONr_long_range_B_other2.5639.7142090
X-RAY DIFFRACTIONr_rigid_bond_restr7.45633429
X-RAY DIFFRACTIONr_sphericity_free23.081576
X-RAY DIFFRACTIONr_sphericity_bonded6.85453590
LS refinement shellResolution: 0.95→0.974 Å
Num. reflection% reflection
Rfree340 -
Rwork6436 -
obs-58.07 %

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