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- PDB-2vi1: Atomic resolution (1.04 A) structure of purified thaumatin I grow... -

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Basic information

Entry
Database: PDB / ID: 2vi1
TitleAtomic resolution (1.04 A) structure of purified thaumatin I grown in sodium D-tartrate at 22 C.
ComponentsTHAUMATIN-1
KeywordsPLANT PROTEIN / KINETICS OF CRYSTALLIZATION / CHIRALITY / TEMPERATURE / MICROBATCH / SWEET PROTEIN
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: 1.04 Å
AuthorsJakoncic, J. / Asherie, N. / Ginsberg, C.
CitationJournal: Cryst.Growth Des. / Year: 2009
Title: Tartrate Chirality Determines Thaumatin Crystal Habit
Authors: Asherie, N. / Jakoncic, J. / Ginsberg, C. / Greenbaum, A. / Stojanoff, V. / Hrnjez, B.J. / Blass, S. / Berger, J.
History
DepositionNov 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THAUMATIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5034
Polymers22,2271
Non-polymers2763
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.939, 54.304, 70.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein THAUMATIN-1 / / THAUMATIN / THAUMATIN I


Mass: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FROM ARIL COVERING SEEDS / Source: (natural) THAUMATOCOCCUS DANIELLII (katemfe) / References: UniProt: P02883
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 1.8 Å3/Da / Density % sol: 29.3 % / Description: NONE
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.1
Details: MICROBATCH METHOD; PROTEIN AT 45 MG/ML IN 10MM SODIUM PHOSPHATE WITH 0.25M SODIUM D-TARTRATE (PH=7.1) AND 10% (V/V) GLYCEROL; CRYSTALS GROWN AT 22 C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8209
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 23, 2007 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8209 Å / Relative weight: 1
ReflectionResolution: 1.04→20 Å / Num. obs: 93952 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 36.1
Reflection shellResolution: 1.04→1.06 Å / Redundancy: 6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.2 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KWN

1kwn
PDB Unreleased entry


Resolution: 1.04→16.72 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.565 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.14 4704 5 %RANDOM
Rwork0.128 ---
obs0.129 89156 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.04→16.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 18 308 1877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221746
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9642394
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.54422.32973
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.96315278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.231517
X-RAY DIFFRACTIONr_chiral_restr0.1010.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021380
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2490.2846
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21229
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6651.51123
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.38221797
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9263703
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8994.5583
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.04→1.07 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.209 352
Rwork0.184 6391

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