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

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Basic information

Entry
Database: PDB / ID: 4yea
TitleCrystal structure of cisplatin bound to a human copper chaperone (dimer) - new refinement
ComponentsCopper transport protein ATOX1
KeywordsMETAL TRANSPORT / Re-refinement of 3iwx / 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 export / copper ion transport / Detoxification of Reactive Oxygen Species / cuprous ion binding / intracellular copper ion homeostasis / ATPase binding ...metallochaperone activity / Ion influx/efflux at host-pathogen interface / copper-dependent protein binding / copper chaperone activity / copper ion export / copper ion transport / Detoxification of Reactive Oxygen Species / cuprous ion binding / intracellular copper ion homeostasis / ATPase binding / response to oxidative stress / copper ion binding / negative regulation of apoptotic process / 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
COPPER (II) ION / Copper transport protein ATOX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.14 Å
AuthorsShabalin, I.G. / Dauter, Z. / Jaskolski, M. / Minor, W. / 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 18, 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 / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn
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 / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_label_seq_id
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
B: Copper transport protein ATOX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9156
Polymers14,5632
Non-polymers3524
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-44 kcal/mol
Surface area7100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.289, 78.289, 54.335
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 7281.451 Da / Num. of mol.: 2
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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.5 M LITHIUM SULFATE, 0.1M MES, 50 MM NACL, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 10562 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 23.4
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

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

3iwx


Resolution: 2.14→25.63 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2055 / WRfactor Rwork: 0.162 / FOM work R set: 0.8799 / SU B: 7.506 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1601 / SU Rfree: 0.1453 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.145 / 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 COMPLEX ...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 3IWX (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
Rfree0.1974 503 4.8 %RANDOM
Rwork0.1602 ---
obs0.1621 10030 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.1 Å2 / Biso mean: 36.165 Å2 / Biso min: 23.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å2-0 Å2
2--0.1 Å20 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 2.14→25.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 16 112 1140
Biso mean--51.37 47.26 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191046
X-RAY DIFFRACTIONr_bond_other_d0.0020.021025
X-RAY DIFFRACTIONr_angle_refined_deg1.4692.0131402
X-RAY DIFFRACTIONr_angle_other_deg0.8843.0032383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9375134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2852635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7515203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.048152
X-RAY DIFFRACTIONr_chiral_restr0.0820.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021121
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02189
X-RAY DIFFRACTIONr_mcbond_it0.6271.648536
X-RAY DIFFRACTIONr_mcbond_other0.6241.646535
X-RAY DIFFRACTIONr_mcangle_it1.0152.465667
X-RAY DIFFRACTIONr_sphericity_bonded17.8180.11
LS refinement shellResolution: 2.143→2.198 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 36 -
Rwork0.206 726 -
all-762 -
obs--99.74 %
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)
11.0921-2.80370.840310.0651-1.31333.73980.06740.2286-0.0842-0.326-0.27370.1482-0.1603-0.08670.20620.10030.0016-0.01920.15240.00220.216719.758-4.2391.204
218.46966.84453.91912.63647.46364.4095-0.0509-0.5514-0.37390.81320.00170.08330.4850.00520.04920.1630.01830.00720.16720.02780.173624.616-9.3729.126
34.16140.98621.99435.03461.42748.2591-0.1147-0.1477-0.02270.19430.1121-0.012-0.0803-0.2390.00250.12430.01870.01040.0750.03230.148419.505-4.127.746
41.6792-0.8536-2.215412.32351.17593.94330.00290.02220.41550.54890.03260.2-0.306-0.3377-0.03550.23050.1057-0.09230.1734-0.10510.406119.8544.0327.262
58.2729-6.5192.975819.62996.79689.00510.10860.4560.5071-0.2368-0.0295-0.7434-0.21470.4176-0.07910.1193-0.0195-0.00630.09180.03050.250628.3242.042.952
613.0633-12.38042.844917.12210.0285.2581-0.1824-0.172-0.08820.05690.15030.2733-0.3387-0.08350.03210.1623-0.03250.04040.05610.05460.155321.4360.666-1.287
714.20423.50885.61034.88890.34424.6256-0.16270.12180.0773-0.12370.0955-0.01640.21890.11660.06720.23590.02180.01980.12830.01260.074639.397-20.1915.491
88.84551.8841.10066.6145-0.01023.0444-0.06270.28580.21630.00940.07350.2596-0.2965-0.0853-0.01090.15270.00950.02170.10380.01210.11532.167-13.748-2.177
95.38114.0587-1.64898.4606-2.06113.9671-0.13180.049-0.0467-0.3050.0546-0.1933-0.02170.16670.07710.1637-0.0092-0.00260.14540.01120.089238.565-17.839-1.22
104.40692.47831.34724.656-0.24792.5444-0.12080.2550.0116-0.1130.2868-0.4501-0.02760.2836-0.16610.1333-0.025-0.00080.1688-0.01950.157144.895-14.4015.018
1120.263-3.05370.81853.22850.32042.58630.08270.30010.9076-0.086-0.04810.1489-0.2091-0.1652-0.03450.1321-0.00010.01720.11990.00860.132534.095-12.8758.435
129.606-2.2659-2.25688.1811-0.69675.39490.09020.712-0.2337-0.02320.0848-0.69130.79130.5213-0.17510.28040.0486-0.05070.2678-0.07040.13445.793-23.0419.037
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 15
2X-RAY DIFFRACTION2A16 - 22
3X-RAY DIFFRACTION3A23 - 38
4X-RAY DIFFRACTION4A39 - 47
5X-RAY DIFFRACTION5A48 - 57
6X-RAY DIFFRACTION6A58 - 68
7X-RAY DIFFRACTION7B2 - 11
8X-RAY DIFFRACTION8B12 - 23
9X-RAY DIFFRACTION9B24 - 38
10X-RAY DIFFRACTION10B39 - 54
11X-RAY DIFFRACTION11B55 - 63
12X-RAY DIFFRACTION12B64 - 68

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