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- PDB-5k08: RecA mini intein-Zeise's salt complex -

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Basic information

Entry
Database: PDB / ID: 5k08
TitleRecA mini intein-Zeise's salt complex
ComponentsRecA mini intein
KeywordsHYDROLASE / cisplatin / Zeise's salt / inhibitor / intein / complex
Function / homology
Function and homology information


DNA strand invasion / DNA strand exchange activity / UV protection / intron homing / intein-mediated protein splicing / recombinational repair / SOS response / ATP-dependent DNA damage sensor activity / ATP-dependent activity, acting on DNA / DNA endonuclease activity ...DNA strand invasion / DNA strand exchange activity / UV protection / intron homing / intein-mediated protein splicing / recombinational repair / SOS response / ATP-dependent DNA damage sensor activity / 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
3,3',3''-phosphanetriyltripropanoic acid / Trichloro(ethene)platinate(II) / Protein RecA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.401 Å
AuthorsLi, Z. / Li, H.M.
Funding support United States, 3items
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
National Institutes of Health/National Cancer Institute (NIH/NCI)CA039442 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.M. / Li, Z. / Zhang, J. / Lippard, S. / Belfort, G. / Shekhtman, A. / Li, H.M. / Belfort, M.
History
DepositionMay 17, 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 4, 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

Downloads & links

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Assembly

Deposited unit
A: RecA mini intein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6735
Polymers15,6681
Non-polymers1,0054
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.687, 63.930, 37.307
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein RecA mini intein


Mass: 15667.825 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P9WHJ3*PLUS
#2: Chemical ChemComp-ZPT / Trichloro(ethene)platinate(II) / Zeise's salt / Zeise's salt


Mass: 329.490 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4Cl3Pt
#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.: 127 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 54%-59% (w/v) ammonium sulfate, 0.1 M Tris, pH 8.5, 2 mM Zeise's salt, 2 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.07136 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07136 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. obs: 27687 / % possible obs: 99.4 % / Redundancy: 13.5 % / Biso Wilson estimate: 17.54 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.025 / Rrim(I) all: 0.091 / Χ2: 2.735 / Net I/av σ(I): 58.569 / Net I/σ(I): 10.8 / Num. measured all: 373588
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.4-1.4210.40.913196
1.42-1.4510.90.805196.6
1.45-1.4811.40.71198.4
1.48-1.51120.61199
1.51-1.5412.90.521199.9
1.54-1.5813.80.4771100
1.58-1.6214.20.4311100
1.62-1.6614.30.3651100
1.66-1.7114.40.3031100
1.71-1.7614.40.2461100
1.76-1.8314.40.1951100
1.83-1.914.40.1521100
1.9-1.9914.30.1261100
1.99-2.0914.40.1011100
2.09-2.2214.40.0921100
2.22-2.3914.40.0851100
2.39-2.6314.30.0821100
2.63-3.0214.20.0741100
3.02-3.813.70.066199.9
3.8-10012.30.071198.4

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5I0A

5i0a


Resolution: 1.401→32.222 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2099 3748 7.24 %
Rwork0.18 --
obs0.1822 51783 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.79 Å2 / Biso mean: 29.2933 Å2 / Biso min: 14.89 Å2
Refinement stepCycle: final / Resolution: 1.401→32.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 18 127 1248
Biso mean--58.88 38.51 -
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)
11.3264-1.098-1.83613.15842.99549.92550.06140.01820.169-0.2508-0.03710.1008-0.5049-0.0949-0.04380.1828-0.0415-0.02990.1196-0.00450.1972-21.5459.9764-4.8205
21.85371.13330.04285.7937-0.72946.1273-0.09420.12960.1824-0.17020.06780.0772-0.25180.35580.04890.1947-0.0331-0.02940.132-0.01790.1548-15.783412.4183-1.9368
31.8151-0.9367-0.5196.7551-2.03395.8656-0.00070.10510.0773-0.7463-0.03670.2275-0.28150.32260.05550.261-0.0329-0.04410.14-0.01590.1278-17.99063.2717-16.5602
45.716-2.37523.0049.3479-5.83712.02080.09390.4419-0.1996-0.5142-0.2387-0.43860.07760.86310.19030.2190.01810.0310.2763-0.03790.1522-8.295-2.126-11.4426
54.3433-0.8909-0.35959.33093.11854.42630.05870.4563-0.3562-0.3169-0.01380.09320.52890.1407-0.0730.21580.0389-0.0520.1331-0.02920.176-15.4128-7.3079-10.0137
61.94950.5536-1.07443.99011.08389.55970.0951-0.0026-0.09860.1668-0.11130.55660.549-0.5933-0.0150.18530.0024-0.00860.1415-0.01850.2735-20.69-6.2134-5.6405
70.70630.42531.99591.33641.99246.674-0.27160.34580.1165-0.63850.19840.0472-1.01760.4406-0.02750.452-0.0802-0.02050.23880.0230.1944-15.156211.0276-15.6984
82.02516.69358.14628.32196.17392.0265-0.61010.2660.1927-0.26470.3621-0.0011-0.49780.50850.18890.2407-0.0522-0.00540.2857-0.00660.1712-10.36267.47770.3135
98.0905-3.29462.287.75181.18258.7141-0.29060.25750.8726-0.35520.2507-0.6954-0.69370.8837-0.02230.3263-0.06370.00120.2241-0.00420.2572-11.25455.8273-6.589
102.00022.00012.00012.0002220.36791.402-0.64190.476-1.20280.74860.3716-3.72960.8350.5109-0.21910.12640.8277-0.14540.9157-2.98763.0005-4.3164
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 50 )A16 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 69 )A51 - 69
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 86 )A70 - 86
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 96 )A87 - 96
6X-RAY DIFFRACTION6chain 'A' and (resid 97 through 413 )A97 - 413
7X-RAY DIFFRACTION7chain 'A' and (resid 414 through 425 )A414 - 425
8X-RAY DIFFRACTION8chain 'A' and (resid 426 through 433 )A426 - 433
9X-RAY DIFFRACTION9chain 'A' and (resid 434 through 443 )A434 - 443
10X-RAY DIFFRACTION10chain 'C'C1

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