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Entry
Database: PDB / ID: 4bar
TitleThaumatin from Thaumatococcus daniellii structure in complex with the europium tris-hydroxyethyltriazoledipicolinate complex at 1.20 A resolution.
ComponentsTHAUMATIN-1
KeywordsPLANT PROTEIN / CLICK-CHEMISTRY / DE NOVO PHASING / EXPERIMENTAL PHASING / LANTHANIDE COMPLEX / ANOMALOUS SCATTERING
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-IKX / Thaumatin I
Similarity search - Component
Biological speciesTHAUMATOCOCCUS DANIELLII (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 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 / Derived calculations
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Mar 25, 2015Group: Database references
Revision 2.0Apr 11, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conf / struct_conn / struct_conn_type / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length
Revision 2.1Dec 19, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 2.2Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THAUMATIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2205
Polymers22,2271
Non-polymers9934
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.852, 57.852, 150.215
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-302-

IKX

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Components

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


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-IKX / 4-(4-(2-hydroxyethyl)-1H-1,2,3-triazol-1-yl)pyridine-2,6-dicarboxylic acid


Mass: 280.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12N4O5
#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.: 411 / 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: 2.83 Å3/Da / Density % sol: 56.5 %
Description: MAD DATA AT TWO WAVELENGTHS WERE COLLECTED. THE FIRST DATA SET AT THE EUROPIUM LIII EDGE AND THE SECOND ONE AT THE SELENIUM K EDGE
Crystal growTemperature: 293 K / pH: 6.5
Details: 0.1 M BIS-TRIS PROPANE PH 6.5, 0.3-0.9 M SODIUM POTASSIUM TARTRATE, 0.0006 M PROTEIN, 0.0014 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 315 / 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: 1.2→45.83 Å / Num. obs: 78373 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 9.9 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.4
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 10 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.7 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALA3.3.16data scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.2→31.499 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 12.29 / Stereochemistry target values: ML
Details: ACCORDING TO THE HIGH RESOLUTION, ANISOTROPIC ADP REFINEMENT WAS APPLIED FOR ALL ATOMS. LIGAND OCCUPANCIES WERE FIXED ACCORDING TO THE LANTHANIDE ION OCCUPANCIES
RfactorNum. reflection% reflection
Rfree0.1553 3920 5 %
Rwork0.1369 --
obs0.1379 78332 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.64 Å2 / ksol: 0.397 e/Å3
Displacement parametersBiso mean: 11.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.8311 Å20 Å20 Å2
2--0.8311 Å20 Å2
3----1.6621 Å2
Refinement stepCycle: LAST / Resolution: 1.2→31.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 61 411 2023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141698
X-RAY DIFFRACTIONf_angle_d1.6122298
X-RAY DIFFRACTIONf_dihedral_angle_d19.032645
X-RAY DIFFRACTIONf_chiral_restr0.099235
X-RAY DIFFRACTIONf_plane_restr0.01306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1999-1.21450.21081340.17082537X-RAY DIFFRACTION94
1.2145-1.22990.19291330.162575X-RAY DIFFRACTION95
1.2299-1.24610.17981310.14952538X-RAY DIFFRACTION95
1.2461-1.26310.13521350.14112585X-RAY DIFFRACTION95
1.2631-1.28120.17981350.13392575X-RAY DIFFRACTION96
1.2812-1.30030.1641340.13212567X-RAY DIFFRACTION96
1.3003-1.32060.19461360.13222611X-RAY DIFFRACTION96
1.3206-1.34230.1541370.12632582X-RAY DIFFRACTION96
1.3423-1.36540.14951390.11562590X-RAY DIFFRACTION96
1.3654-1.39030.16321380.11412612X-RAY DIFFRACTION96
1.3903-1.4170.14741380.11282612X-RAY DIFFRACTION97
1.417-1.44590.12951370.10772609X-RAY DIFFRACTION97
1.4459-1.47740.1681370.10362622X-RAY DIFFRACTION97
1.4774-1.51170.14121400.10352634X-RAY DIFFRACTION97
1.5117-1.54950.13311400.09412639X-RAY DIFFRACTION97
1.5495-1.59140.12931410.09492643X-RAY DIFFRACTION97
1.5914-1.63830.12031430.0972656X-RAY DIFFRACTION97
1.6383-1.69110.13541410.09852661X-RAY DIFFRACTION98
1.6911-1.75160.13331380.1062679X-RAY DIFFRACTION98
1.7516-1.82170.13981410.11362688X-RAY DIFFRACTION98
1.8217-1.90460.1421430.12032680X-RAY DIFFRACTION98
1.9046-2.0050.15691450.1192701X-RAY DIFFRACTION98
2.005-2.13060.13541420.13022726X-RAY DIFFRACTION99
2.1306-2.2950.16411450.13162729X-RAY DIFFRACTION99
2.295-2.52590.15591470.14692763X-RAY DIFFRACTION99
2.5259-2.89120.17661470.16022784X-RAY DIFFRACTION99
2.8912-3.64180.16461490.15682841X-RAY DIFFRACTION100
3.6418-31.510.16091540.18212973X-RAY DIFFRACTION98

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