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- PDB-4ydx: Crystal structure of cisplatin bound to a human copper chaperone ... -

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Basic information

Entry
Database: PDB / ID: 4ydx
TitleCrystal structure of cisplatin bound to a human copper chaperone (monomer) - new refinement
ComponentsCopper transport protein ATOX1
KeywordsMETAL TRANSPORT / Re-refinement of 3iwl / cisplatin / platinum / Metal-binding
Function / homology
Function and homology information


metallochaperone activity / Ion influx/efflux at host-pathogen interface / copper-dependent protein binding / copper chaperone activity / copper ion transport / Detoxification of Reactive Oxygen Species / cuprous ion binding / intracellular copper ion homeostasis / response to oxidative stress / copper ion binding / cytosol
Similarity search - Function
Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 3,3',3''-phosphanetriyltripropanoic acid / Copper transport protein ATOX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.602 Å
AuthorsShabalin, I.G. / Boal, A.K. / Dauter, Z. / Jaskolski, M. / Minor, W. / Rosenzweig, A.C. / Wlodawer, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.
Authors: Shabalin, I. / Dauter, Z. / Jaskolski, M. / Minor, W. / Wlodawer, A.
#1: Journal: J.Am.Chem.Soc. / Year: 2009
Title: Crystal structures of cisplatin bound to a human copper chaperone.
Authors: Boal, A.K. / Rosenzweig, A.C.
History
DepositionFeb 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Sep 9, 2015Group: Database references
Revision 1.3Sep 16, 2015Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.6Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper transport protein ATOX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8234
Polymers7,2811
Non-polymers5413
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.070, 54.070, 55.578
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

21A-216-

HOH

31A-236-

HOH

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Components

#1: Protein Copper transport protein ATOX1 / Metal transport protein ATX1


Mass: 7281.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATOX1, HAH1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00244
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid / TCEP


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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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: 3.22 Å3/Da / Density % sol: 61.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2M lithium sulfate, 0.1M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.90511 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90511 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 13182 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 19.5 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 24.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 3.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
SHARPphasing
Cootmodel building
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3iwl

3iwl


Resolution: 1.602→27.03 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.1805 / WRfactor Rwork: 0.1549 / FOM work R set: 0.9153 / SU B: 2.348 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0574 / SU Rfree: 0.0582 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. This deposit resulted from an analysis of a number of PDB entries that contain cisplatin or carboplatin in ...Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. This deposit resulted from an analysis of a number of PDB entries that contain cisplatin or carboplatin in complex with proteins, conducted in the spirit of the Terwilliger-Bricogne motto advocating continuous improvement of the macromolecular models in the PDB (Acta Cryst. D70, 2533, 2014). The structure factors and coordinates, originally deposited as 3iwl (Boal, A. K. & Rosenzweig, A. C. 2009. J. Am. Chem. Soc. 131, 14196-14197), were used as the starting point for an independent re-refinement. The new model includes some reinterpretation of the ligands, has lower R factors, and improved statistics describing the agreement with the experimental data.
RfactorNum. reflection% reflectionSelection details
Rfree0.1555 621 4.9 %RANDOM
Rwork0.136 ---
obs0.1369 12057 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.2 Å2 / Biso mean: 22.116 Å2 / Biso min: 12.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 1.602→27.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms503 0 22 96 621
Biso mean--34.09 39.65 -
Num. residues----67
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.019548
X-RAY DIFFRACTIONr_bond_other_d0.0020.02530
X-RAY DIFFRACTIONr_angle_refined_deg1.5152.03732
X-RAY DIFFRACTIONr_angle_other_deg0.9133.0031235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.603570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15625.26319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50515103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.24152
X-RAY DIFFRACTIONr_chiral_restr0.0930.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02590
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02100
X-RAY DIFFRACTIONr_mcbond_it0.4870.99271
X-RAY DIFFRACTIONr_mcbond_other0.4620.985270
X-RAY DIFFRACTIONr_mcangle_it0.8121.478338
X-RAY DIFFRACTIONr_rigid_bond_restr1.57231
X-RAY DIFFRACTIONr_sphericity_bonded14.6890.12
LS refinement shellResolution: 1.602→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 44 -
Rwork0.216 858 -
all-902 -
obs--97.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
116.326113.16832.318428.59488.05265.6487-0.30190.3017-0.3642-0.72050.16470.2758-0.0845-0.27130.13710.0871-0.01580.01310.0782-0.00260.034525.2048.9415.515
27.16335.4498-3.274112.0904-6.62838.22080.1771-0.10090.30540.4787-0.15290.0426-0.71370.0919-0.02430.0938-0.03-0.01010.0283-0.01520.073934.17422.36814.395
34.96090.97810.28368.71420.3144.463-0.06170.11650.1892-0.10150.0347-0.1305-0.20660.27750.0270.0512-0.0422-0.01610.04170.01420.054837.56518.4987.275
45.7675-0.48680.157311.0049-0.24935.21270.02580.1757-0.0276-0.2806-0.1991-0.3991-0.06750.41260.17340.02210.00410.00140.05230.00070.069238.4568.9967.167
53.3019-1.3413-0.290711.86723.92995.1414-0.00640.0413-0.0117-0.0806-0.14420.4664-0.258-0.13840.15050.0639-0.0060.00220.03570.00960.033528.33216.7968.909
62.85291.42390.326541.2432.74131.25950.0117-0.1106-0.25020.2833-0.1750.9108-0.0761-0.14060.16340.0801-0.00880.02560.0590.00020.084326.8178.92211.962
74.74973.487-2.14785.9629-0.65633.0868-0.1407-0.2596-0.28550.16270.0132-0.1560.06950.1340.12750.07640.0183-0.00340.07990.01340.10233.9835.3817.75
811.64057.37080.705911.4091.12656.889-0.0354-0.2956-0.07740.1227-0.036-0.2943-0.16430.23220.07130.0392-0.035-0.02870.0779-0.00880.065139.58514.6616.537
917.23868.1795-4.30238.317-2.82384.427-0.09980.22730.0880.15510.27480.2607-0.1825-0.2319-0.17510.06050.0051-0.0050.07050.01280.029426.92912.87719.968
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 6
2X-RAY DIFFRACTION2A7 - 12
3X-RAY DIFFRACTION3A13 - 20
4X-RAY DIFFRACTION4A21 - 28
5X-RAY DIFFRACTION5A29 - 38
6X-RAY DIFFRACTION6A39 - 45
7X-RAY DIFFRACTION7A46 - 54
8X-RAY DIFFRACTION8A55 - 60
9X-RAY DIFFRACTION9A61 - 68

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