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- PDB-4tvt: New ligand for thaumatin discovered using acoustic high throughpu... -

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Basic information

Entry
Database: PDB / ID: 4tvt
TitleNew ligand for thaumatin discovered using acoustic high throughput screening
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / acoustic
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
ASCORBIC ACID / L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsTeplitsky, E. / Joshi, K. / Ericson, D.L. / Scalia, A. / Mullen, J.D. / Sweet, R.M. / Soares, A.S.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)11-008 United States
Department of Energy (DOE, United States)P41RR012408 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103473 United States
CitationJournal: J.Struct.Biol. / Year: 2015
Title: High throughput screening using acoustic droplet ejection to combine protein crystals and chemical libraries on crystallization plates at high density.
Authors: Teplitsky, E. / Joshi, K. / Ericson, D.L. / Scalia, A. / Mullen, J.D. / Sweet, R.M. / Soares, A.S.
History
DepositionJun 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_nat ...citation / entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Refinement description
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _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.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_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.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)23,44215
Polymers22,2271
Non-polymers1,21514
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.837, 57.837, 149.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Thaumatin-1 / / Thaumatin I


Mass: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Sugar
ChemComp-ASC / ASCORBIC ACID / Vitamin C / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: medication*YM
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 1.5M NaK Tartrate, 0.1M Bis Tris pH 6.6 / PH range: 6.5-6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.2→53.95 Å / Num. all: 68461 / Num. obs: 68461 / % possible obs: 89.83 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 42.81
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 1 / % possible all: 23.6

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1THI

1thi


Resolution: 1.2→53.95 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.547 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16275 3518 4.9 %RANDOM
Rwork0.14461 ---
obs0.1455 68461 89.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.345 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å2-0 Å2
2--0.36 Å2-0 Å2
3----0.71 Å2
Refinement stepCycle: 1 / Resolution: 1.2→53.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 78 442 2071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.021724
X-RAY DIFFRACTIONr_bond_other_d0.0020.021520
X-RAY DIFFRACTIONr_angle_refined_deg2.8671.9952353
X-RAY DIFFRACTIONr_angle_other_deg1.0723.0023522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.1495.158221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24922.68767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01815255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7771514
X-RAY DIFFRACTIONr_chiral_restr0.1790.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212007
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02395
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_it1.6231.244857
X-RAY DIFFRACTIONr_mcbond_other1.5781.24856
X-RAY DIFFRACTIONr_mcangle_it2.3941.8691080
X-RAY DIFFRACTIONr_mcangle_other2.4191.8731081
X-RAY DIFFRACTIONr_scbond_it3.8361.574867
X-RAY DIFFRACTIONr_scbond_other3.8421.576864
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7452.2221272
X-RAY DIFFRACTIONr_long_range_B_refined10.04815.2942398
X-RAY DIFFRACTIONr_long_range_B_other9.00512.3092089
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 76 -
Rwork0.405 1539 -
obs--27.69 %

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