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- PDB-6dgb: Crystal structure of the C-terminal catalytic domain of IS1535 Tn... -

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Basic information

Entry
Database: PDB / ID: 6dgb
TitleCrystal structure of the C-terminal catalytic domain of IS1535 TnpA, an IS607-like serine recombinase
ComponentsIS607 family transposase IS1535
KeywordsHYDROLASE / 607-like serine recombinase
Function / homology
Function and homology information


DNA strand exchange activity / DNA binding
Similarity search - Function
IS607-like transposase, catalytic domain / Resolvase, N-terminal catalytic domain / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IS607 family transposase IS1535 / Possible resolvase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.52 Å
AuthorsChen, W.Y. / Hancock, S.P. / Cascio, D. / Johnson, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM038509 United States
CitationJournal: Elife / Year: 2018
Title: Multiple serine transposase dimers assemble the transposon-end synaptic complex during IS607-family transposition.
Authors: Chen, W. / Mandali, S. / Hancock, S.P. / Kumar, P. / Collazo, M. / Cascio, D. / Johnson, R.C.
History
DepositionMay 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: IS607 family transposase IS1535
B: IS607 family transposase IS1535


Theoretical massNumber of molelcules
Total (without water)31,4882
Polymers31,4882
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-30 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.560, 54.180, 104.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein IS607 family transposase IS1535 / Resolvase


Mass: 15744.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: IS1535 TnpA / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A045HV29, UniProt: I6WZS4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 8, 2015
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→48.08 Å / Num. obs: 10275 / % possible obs: 95.2 % / Redundancy: 4.328 % / Biso Wilson estimate: 54.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.112 / Χ2: 1.045 / Net I/σ(I): 6.48 / Num. measured all: 44467 / Scaling rejects: 73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.573.9620.6481.57110.8460.74491.4
2.57-2.644.3640.5321.857420.9320.60597.8
2.64-2.714.5850.4482.177260.9570.50497.8
2.71-2.84.4370.4192.527160.9420.47497.8
2.8-2.894.4590.3552.956640.9610.40396.9
2.89-2.994.3660.2953.446590.9540.33597.2
2.99-3.14.2790.2114.126210.9870.23995.4
3.1-3.234.2270.1785.365980.9780.20294.5
3.23-3.374.490.146.765880.9950.15896.4
3.37-3.544.5120.1297.965700.9930.14697.3
3.54-3.734.3230.0989.35290.9940.11195.7
3.73-3.964.2610.08710.125100.9950.09895.9
3.96-4.234.150.07611.134520.9950.08690.6
4.23-4.574.4450.08612.254470.9940.09696.1
4.57-54.3980.0911.994150.9930.10195.4
5-5.594.2790.08812.233760.9930.09993.8
5.59-6.464.1640.08311.853110.9910.09388.9
6.46-7.914.3110.06313.022860.9990.0792.9
7.91-11.194.0410.06313.712220.9970.07191.4
11.19-48.083.7050.05812.351320.9980.06786.8

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Processing

Software
NameVersionClassification
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
SHELXDEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.52→48.08 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.363
RfactorNum. reflection% reflectionSelection details
Rfree0.261 365 4.59 %RANDOM
Rwork0.228 ---
obs0.23 7951 75.3 %-
Displacement parametersBiso max: 132.86 Å2 / Biso mean: 49.97 Å2 / Biso min: 8.38 Å2
Baniso -1Baniso -2Baniso -3
1-17.0946 Å20 Å20 Å2
2---19.2881 Å20 Å2
3---2.1935 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.52→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 0 24 2026
Biso mean---28.87 -
Num. residues----265
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d732SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes310HARMONIC5
X-RAY DIFFRACTIONt_it2017HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion260SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2244SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2017HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2714HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion18.39
LS refinement shellResolution: 2.52→2.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.285 47 4.66 %
Rwork0.2593 962 -
all0.2604 1009 -
obs--34.5 %
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)
11.62910.5470.45892.42812.95994.2322-0.0750.1078-0.19560.13960.0691-0.30990.31560.03080.00590.2839-0.0218-0.0589-0.32120.05070.004713.1566-9.802550.4951
22.61940.8646-0.5612.1523-2.90541.93020.05370.06770.32890.23460.03380.4309-0.39960.0881-0.08760.3108-0.04230.0414-0.3253-0.0663-0.010811.52669.90950.2351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A52 - 189
2X-RAY DIFFRACTION2{ B|* }B51 - 188

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