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- PDB-1rqw: Thaumatin Structure at 1.05 A Resolution -

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Basic information

Entry
Database: PDB / ID: 1rqw
TitleThaumatin Structure at 1.05 A Resolution
Componentsthaumatin I
KeywordsPLANT PROTEIN / thaumatin / x-ray structure
Function / homology
Function and homology information


defense response / cytoplasmic vesicle / extracellular region
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
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsMa, Q. / Sheldrick, G.M.
CitationJournal: To be Published
Title: Thaumatin Structure at 1.05 A Resolution
Authors: Ma, Q. / Sheldrick, G.M.
History
DepositionDec 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 25, 2012Group: Structure summary
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Apr 3, 2024Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: thaumatin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3932
Polymers22,2431
Non-polymers1501
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.847, 57.847, 150.125
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1282-

HOH

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Components

#1: Protein thaumatin I


Mass: 22243.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE TWO ISOFORMS OF THAUMATION, I AND II. LYS46 FROM THE FORM I IS USED BECAUSE THE ...THERE ARE TWO ISOFORMS OF THAUMATION, I AND II. LYS46 FROM THE FORM I IS USED BECAUSE THE CRYSTALLIZATION MATERIAL CONTAINS A MIXTURE OF LYS AND ASN. ASP IS USED AT POSITION 113 AS SUGGESTED BY KO ET AL., ACTA CRYST. D50,813(1994)

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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: 2.23 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 298 K / pH: 6.8
Details: Drop: 4ul 40mg/ml thaumatin (in DTNB saturated ddH2O) + 2ul well solution [0.05M ADA pH6.8, 0.6M potassium sodium tartrate (whose 2M stock soution is saturated with DTNB), 20% Glycerol, ...Details: Drop: 4ul 40mg/ml thaumatin (in DTNB saturated ddH2O) + 2ul well solution [0.05M ADA pH6.8, 0.6M potassium sodium tartrate (whose 2M stock soution is saturated with DTNB), 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M06X / Wavelength: 1.5418
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Feb 10, 2003 / Details: OSMIC BLUE CONFOCAL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.05→160 Å / Num. obs: 116807 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 19.1 % / Rsym value: 0.039 / Net I/σ(I): 37.8
Reflection shellResolution: 1.05→1.15 Å / Redundancy: 9.25 % / Mean I/σ(I) obs: 7.17 / Rsym value: 0.298 / % possible all: 96.5

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Processing

Software
NameClassification
PROTEUM PLUSdata collection
SAINTdata reduction
SADABSdata reduction
XPREPdata reduction
MOLREPphasing
SHELXL-97refinement
PROTEUM PLUSdata reduction
SAINTdata scaling
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN HOUSE MODEL

Resolution: 1.05→10 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.152 5831 -RANDOM
all0.127 116567 --
obs0.127 -97.6 %-
Refine analyzeNum. disordered residues: 17
Refinement stepCycle: LAST / Resolution: 1.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 10 398 1960
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0.016
X-RAY DIFFRACTIONs_from_restr_planes0.439
X-RAY DIFFRACTIONs_zero_chiral_vol0.063
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.053
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.028
X-RAY DIFFRACTIONs_approx_iso_adps0.116

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