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- PDB-5l4r: X-ray structure of the adduct between thaumatin and cisplatin -

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Basic information

Entry
Database: PDB / ID: 5l4r
TitleX-ray structure of the adduct between thaumatin and cisplatin
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / cisplatin / drug / model 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
bis(azanyl)-chloranyl-oxidanyl-platinum / Cisplatin / L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsRusso Krauss, I. / Ferraro, G. / Merlino, A.
CitationJournal: Inorg.Chem. / Year: 2016
Title: Cisplatin-Protein Interactions: Unexpected Drug Binding to N-Terminal Amine and Lysine Side Chains.
Authors: Russo Krauss, I. / Ferraro, G. / Merlino, A.
History
DepositionMay 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Nov 6, 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)25,85815
Polymers22,2271
Non-polymers3,63114
Water7,620423
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-54 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.837, 57.837, 150.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thaumatin-1 / Thaumatin I


Mass: 22227.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Production host: Escherichia coli (E. coli) / References: UniProt: P02883

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Non-polymers , 5 types, 437 molecules

#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-73M / bis(azanyl)-chloranyl-oxidanyl-platinum


Mass: 279.584 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: ClH5N2OPt
#4: Chemical
ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.82 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 % PEG3350, 0.2 M sodium tartrate. Crystals of the adduct were obtained by soaking procedure, adding 1 uL of cisplatin solution 10 mM to the drop containing thaumatin crystals

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→53.98 Å / Num. obs: 43868 / % possible obs: 94.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 40
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.7 / % possible all: 68

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QY5

3qy5


Resolution: 1.45→53.97 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.966 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.052 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.15369 2147 4.9 %RANDOM
Rwork0.1124 ---
obs0.11444 41675 94.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.169 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0 Å2-0 Å2
2--0.4 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.45→53.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 63 423 2037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.021746
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9041.9782363
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9845218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9722.875
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10115273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3791516
X-RAY DIFFRACTIONr_chiral_restr0.2640.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211339
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.731.513842
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9342.2691055
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.0481.891904
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.35617.1243234
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr9.5731746
X-RAY DIFFRACTIONr_sphericity_free46.27569
X-RAY DIFFRACTIONr_sphericity_bonded18.37752069
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 109 -
Rwork0.302 2375 -
obs--73.56 %

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