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- PDB-5i0a: RecA mini intein in complex with cisplatin -

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Basic information

Entry
Database: PDB / ID: 5i0a
TitleRecA mini intein in complex with cisplatin
ComponentsIntein
KeywordsSPLICING / Inhibitor / cisplatin / intein
Function / homology
Function and homology information


UV protection / DNA strand invasion / intein-mediated protein splicing / intron homing / DNA strand exchange activity / recombinational repair / ATP-dependent DNA damage sensor activity / SOS response / ATP-dependent activity, acting on DNA / DNA endonuclease activity ...UV protection / DNA strand invasion / intein-mediated protein splicing / intron homing / DNA strand exchange activity / recombinational repair / ATP-dependent DNA damage sensor activity / SOS response / ATP-dependent activity, acting on DNA / DNA endonuclease activity / single-stranded DNA binding / manganese ion binding / damaged DNA binding / Hydrolases; Acting on ester bonds / response to antibiotic / DNA damage response / magnesium ion binding / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / LAGLIDADG-like domain / : / : / RecA C-terminal domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / recA signature. / DNA recombination and repair protein RecA ...Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / LAGLIDADG-like domain / : / : / RecA C-terminal domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / recA signature. / DNA recombination and repair protein RecA / recA bacterial DNA recombination protein / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / Beta Complex / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Cisplatin / 3,3',3''-phosphanetriyltripropanoic acid / Protein RecA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsLi, Z. / Zhang, J. / Li, H.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM39422 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM44844 United States
CitationJournal: To be published
Title: Structural insights into protein splicing inhibition by platinum therapeutics as potential anti-microbials
Authors: Chan, H. / Pearson, S. / Green, C. / Li, Z. / Zhang, J. / Lippard, S. / Belfort, G. / Shekhtman, A. / Li, H.M. / Belfort, M.
History
DepositionFeb 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Intein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8585
Polymers15,9121
Non-polymers9464
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.269, 64.051, 37.167
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-772-

HOH

21A-792-

HOH

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Components

#1: Protein Intein


Mass: 15912.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pET45b / Production host: Escherichia coli (E. coli) / References: UniProt: P9WHJ3*PLUS
#2: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication, chemotherapy*YM
#3: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8.5
Details: 58% ammonium sulfate, 0.1M Tris, pH 8.5, 2% isopropanol, 2 mM cisplatin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.0711 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0711 Å / Relative weight: 1
ReflectionResolution: 1.5→100 Å / Num. obs: 22614 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.026 / Rrim(I) all: 0.071 / Χ2: 2.006 / Net I/av σ(I): 43.344 / Net I/σ(I): 12.9 / Num. measured all: 159217
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.536.50.60311120.8750.2550.6571.162100
1.53-1.556.70.53411230.9430.2190.5781.19399.6
1.55-1.5870.5110910.9340.2060.5511.185100
1.58-1.6270.47611160.9520.1920.5141.198100
1.62-1.657.10.43211150.950.1730.4651.223100
1.65-1.697.10.35511240.970.1420.3821.256100
1.69-1.737.20.31710930.9740.1260.3421.295100
1.73-1.787.10.24311190.9850.0970.2621.314100
1.78-1.837.20.20711110.9870.0830.2231.37100
1.83-1.897.10.1611260.990.0650.1731.435100
1.89-1.967.10.12511380.9950.050.1351.486100
1.96-2.047.20.11110960.9960.0440.121.714100
2.04-2.137.10.09111350.9970.0360.0981.878100
2.13-2.247.20.07711120.9970.0310.0832.052100
2.24-2.387.20.06911470.9970.0270.0742.179100
2.38-2.567.20.06511250.9980.0260.072.391100
2.56-2.827.20.05811460.9980.0230.0632.727100
2.82-3.237.10.04711580.9990.0190.0513.093100
3.23-4.0770.0411840.9990.0160.0443.62999.9
4.07-1006.50.04312430.9990.0170.0465.96499.2

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: SAD
Starting model: 2in0

2in0


Resolution: 1.5→37.167 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1928 3761 8.89 %
Rwork0.1703 --
obs0.1724 42316 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.22 Å2 / Biso mean: 22.8474 Å2 / Biso min: 8.28 Å2
Refinement stepCycle: final / Resolution: 1.5→37.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 18 192 1313
Biso mean--54.17 34.65 -
Num. residues----142
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)
10.8648-0.39220.07682.79251.82968.1605-0.0344-0.01680.1529-0.1765-0.03070.2488-0.3512-0.28950.06060.0792-0.0163-0.02810.0870.00080.1754-21.410510.0081-4.8302
21.39991.4338-1.18984.87640.48516.2703-0.32510.24670.397-0.6886-0.04760.738-0.9932-0.37490.23150.2480.0076-0.12650.10910.02550.2422-21.731515.8513-8.226
30.8810.06910.25012.6552.10614.2183-0.09910.0590.1139-0.14550.1629-0.0671-0.30060.4983-0.02760.095-0.038-0.02160.11580.00110.1261-13.95259.3996-5.1547
42.7033-0.37091.20385.1479-1.18174.1392-0.01620.0832-0.1232-0.1464-0.0405-0.0872-0.01590.43360.05240.07480.00020.01340.125-0.01960.0746-13.1671-1.6503-11.6883
55.4385-0.04855.01045.4485-3.24976.5070.08960.346-0.0836-0.4055-0.2735-0.32280.58450.89250.17310.120.05210.03970.2353-0.00880.1441-6.8033-2.9317-11.9626
62.2649-0.8444-0.29875.73972.71986.75030.06490.3064-0.235-0.1498-0.02540.17120.44670.1746-0.02430.09960.0212-0.03310.107-0.02520.1339-15.1788-7.1715-10.0483
71.77130.3999-0.74252.98290.56666.66890.0368-0.0477-0.05430.1972-0.0190.53790.3847-0.4152-0.02270.1380.01380.01070.093-0.00780.24-20.5021-6.1561-5.701
80.4558-0.5221-0.3311.55960.991.4098-0.09740.21290.1312-0.59940.0244-0.007-0.83590.28760.06670.3516-0.0751-0.01050.19980.01470.1419-14.87811.0558-15.6858
97.65032.94944.18393.93462.7035.9031-0.4267-0.21930.0587-0.18890.3493-0.2119-0.51290.78640.06650.1033-0.034-0.0140.2234-0.01490.1391-10.20557.63340.2628
104.6926-0.73660.35276.7259-0.29264.7104-0.05760.03920.3486-0.12410.0274-0.6234-0.38860.68530.00990.126-0.03330.00950.1852-0.00130.1492-11.15996.0123-6.3268
112.00461.9982.00152.00441.99852.00010.71560.66150.0836-0.0922-0.007-0.1674-1.1505-0.6871-0.71410.32250.11140.62320.85290.26490.9312-2.76633.4762-4.3504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )A1 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 24 )A16 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 61 )A25 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 79 )A62 - 79
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 86 )A80 - 86
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 96 )A87 - 96
7X-RAY DIFFRACTION7chain 'A' and (resid 97 through 413 )A97 - 413
8X-RAY DIFFRACTION8chain 'A' and (resid 414 through 425 )A414 - 425
9X-RAY DIFFRACTION9chain 'A' and (resid 426 through 433 )A426 - 433
10X-RAY DIFFRACTION10chain 'A' and (resid 434 through 443 )A434 - 443
11X-RAY DIFFRACTION11chain 'C'C1

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