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- PDB-4bal: Thaumatin from Thaumatococcus daniellii structure in complex with... -

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Basic information

Entry
Database: PDB / ID: 4bal
TitleThaumatin from Thaumatococcus daniellii structure in complex with the europium tris-hydroxymethyltriazoledipicolinate complex at 1.30 A resolution.
ComponentsTHAUMATIN-1
KeywordsPLANT PROTEIN / CLICK-CHEMISTRY / ANOMALOUS SCATTERING / DE NOVO PHASING / EXPERIMENTAL PHASING / DIPICOLINATE
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
EUROPIUM (III) ION / Chem-HM6 / Thaumatin I
Similarity search - Component
Biological speciesTHAUMATOCOCCUS DANIELLII (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.298 Å
AuthorsTalon, R. / Kahn, R. / Gautier, A. / Nauton, L. / Girard, E.
Citation
Journal: Chem.Commun.(Camb.) / Year: 2012
Title: Clicked Europium Dipicolinate Complexes for Protein X-Ray Structure Determination.
Authors: Talon, R. / Nauton, L. / Canet, J.-L. / Kahn, R. / Girard, E. / Gautier, A.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2008
Title: Protein Crystallography Through Supramolecular Interactions between a Lanthanide Complex and Arginine.
Authors: Pompidor, G. / D'Aleo, A. / Vicat, J. / Toupet, L. / Giraud, N. / Kahn, R. / Maury, O.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: A Dipicolinate Lanthanide Complex for Solving Protein Structures Using Anomalous Diffraction.
Authors: Pompidor, G. / Maury, O. / Vicat, J. / Kahn, R.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Gd-Hpdo3A, a Complex to Obtain High-Phasing-Power Heavy-Atom Derivatives for Sad and MAD Experiments: Results with Tetragonal Hen Egg-White Lysozyme.
Authors: Girard, E. / Chantalat, L. / Vicat, J. / Kahn, R.
History
DepositionSep 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 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
Revision 1.5Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1725
Polymers22,2271
Non-polymers9454
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.988, 57.988, 150.184
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-1210-

HM6

21A-1211-

EU3

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Components

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


Mass: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SIGMA-ALDRICH POWDER, CATALOG REFERENCE T7638 / Source: (natural) THAUMATOCOCCUS DANIELLII (katemfe) / References: UniProt: P02883
#2: Chemical ChemComp-HM6 / 4-(4-(hydroxymethyl)-1h-1,2,3-triazol-1-yl)pyridine-2,6-dicarboxylic acid / HYDROXYMETHYLTRIAZOLE DIPICOLINIC ACID


Mass: 264.194 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H8N4O5
#3: Chemical ChemComp-EU3 / EUROPIUM (III) ION


Mass: 151.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Eu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.37 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growTemperature: 293 K / pH: 6.5
Details: 0.1 M BIS-TRIS PROPANE PH 6.5, 0.3-0.9 SODIUM POTASSIUM TARTRATE, 0.0006 M PROTEIN, 0.010 M LANTHANIDE COMPLEX, 293 K, 5 DAYS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2010 / Details: MIRRORS
RadiationMonochromator: EITHER 111 OR 311 SILICON SINGLE CRISTALS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.3→45.9 Å / Num. obs: 64239 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 6.6 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.5
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSJANUARY 30 2009data reduction
SCALA3.316data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BAR

4bar


Resolution: 1.298→28.994 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 11.87 / Stereochemistry target values: ML
Details: ACCORDING TO THE HIGH RESOLUTION, ANISOTROPIC ADP REFINEMENT WAS APPLIED FOR ALL ATOMS. LIGANDS OCCUPANCIES WERE FIXED ACCORDING TO THE LANTHANIDE ION OCCUPANCY.
RfactorNum. reflection% reflection
Rfree0.1574 3207 5 %
Rwork0.135 --
obs0.1362 64138 99.88 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.309 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso mean: 11.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.3483 Å20 Å20 Å2
2--0.3483 Å20 Å2
3----0.6966 Å2
Refinement stepCycle: LAST / Resolution: 1.298→28.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 58 376 1985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011695
X-RAY DIFFRACTIONf_angle_d1.2682295
X-RAY DIFFRACTIONf_dihedral_angle_d21.42642
X-RAY DIFFRACTIONf_chiral_restr0.083235
X-RAY DIFFRACTIONf_plane_restr0.007306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2983-1.31770.21131340.19462554X-RAY DIFFRACTION98
1.3177-1.33820.22261370.17112599X-RAY DIFFRACTION100
1.3382-1.36020.18531370.16662592X-RAY DIFFRACTION100
1.3602-1.38360.17721370.14882620X-RAY DIFFRACTION100
1.3836-1.40880.18571370.14152599X-RAY DIFFRACTION100
1.4088-1.43590.15061370.13032611X-RAY DIFFRACTION100
1.4359-1.46520.1571390.12152621X-RAY DIFFRACTION100
1.4652-1.49710.15781370.11292599X-RAY DIFFRACTION100
1.4971-1.53190.1491380.10862628X-RAY DIFFRACTION100
1.5319-1.57020.11771380.10282637X-RAY DIFFRACTION100
1.5702-1.61260.12381390.09612617X-RAY DIFFRACTION100
1.6126-1.66010.14561380.09992633X-RAY DIFFRACTION100
1.6601-1.71370.12681380.09942624X-RAY DIFFRACTION100
1.7137-1.77490.13521390.10462627X-RAY DIFFRACTION100
1.7749-1.8460.14731380.10892630X-RAY DIFFRACTION100
1.846-1.930.13051400.11032660X-RAY DIFFRACTION100
1.93-2.03170.10681400.11012649X-RAY DIFFRACTION100
2.0317-2.15890.15511400.12092687X-RAY DIFFRACTION100
2.1589-2.32560.14741410.12462669X-RAY DIFFRACTION100
2.3256-2.55950.15681410.14272689X-RAY DIFFRACTION100
2.5595-2.92950.18351440.15252719X-RAY DIFFRACTION100
2.9295-3.68970.1611440.15192749X-RAY DIFFRACTION100
3.6897-29.00120.18391540.16992918X-RAY DIFFRACTION99

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