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- PDB-6dgc: Crystal structure of the C-terminal catalytic domain of ISC1926 T... -

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Basic information

Entry
Database: PDB / ID: 6dgc
TitleCrystal structure of the C-terminal catalytic domain of ISC1926 TnpA, an IS607-like serine recombinase
ComponentsISC1926 TnpA C-terminal catalytic domain
KeywordsHYDROLASE / IS607-like serine recombinase
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA binding
Similarity search - Function
Helix Hairpins - #2170 / IS607-like transposase, catalytic domain / SinI-like, DNA-binding domain / Helix-turn-helix domain, group 17 / Helix-turn-helix domain / Resolvase, N-terminal catalytic domain / Recombinase, conserved site / Site-specific recombinases active site. / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain ...Helix Hairpins - #2170 / IS607-like transposase, catalytic domain / SinI-like, DNA-binding domain / Helix-turn-helix domain, group 17 / Helix-turn-helix domain / Resolvase, N-terminal catalytic domain / Recombinase, conserved site / Site-specific recombinases active site. / 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 / Putative DNA-binding domain superfamily / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSulfolobus sp. L00 11 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.92 Å
AuthorsHancock, S.P. / Kumar, 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 1.3Oct 11, 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: ISC1926 TnpA C-terminal catalytic domain
B: ISC1926 TnpA C-terminal catalytic domain
C: ISC1926 TnpA C-terminal catalytic domain
D: ISC1926 TnpA C-terminal catalytic domain


Theoretical massNumber of molelcules
Total (without water)66,6534
Polymers66,6534
Non-polymers00
Water0
1
A: ISC1926 TnpA C-terminal catalytic domain
B: ISC1926 TnpA C-terminal catalytic domain


Theoretical massNumber of molelcules
Total (without water)33,3272
Polymers33,3272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-32 kcal/mol
Surface area12840 Å2
MethodPISA
2
C: ISC1926 TnpA C-terminal catalytic domain
D: ISC1926 TnpA C-terminal catalytic domain


Theoretical massNumber of molelcules
Total (without water)33,3272
Polymers33,3272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-26 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.080, 212.320, 61.600
Angle α, β, γ (deg.)90.000, 126.680, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
ISC1926 TnpA C-terminal catalytic domain


Mass: 16663.330 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus sp. L00 11 (acidophilic) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5MPE7

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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: 3.82 Å3/Da / Density % sol: 67.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: Tascimate, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.91→19.72 Å / Num. obs: 19649 / % possible obs: 88.6 % / Redundancy: 3.62 % / Biso Wilson estimate: 84.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.058 / Χ2: 1.058 / Net I/σ(I): 12.85 / Num. measured all: 71134 / Scaling rejects: 106
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.91-2.981.8980.5111.3175616299250.7610.67356.8
2.98-3.063.3910.3872.334720160813920.9590.45486.6
3.06-3.153.7520.3373.015497153214650.970.38995.6
3.15-3.253.7330.2334.045319152214250.9880.26993.6
3.25-3.353.6780.1754.885039144413700.9940.20294.9
3.35-3.473.6770.1526.164780140013000.990.17592.9
3.47-3.63.6270.1138.044512136912440.9940.1390.9
3.6-3.753.5040.09210.044096130811690.9950.10789.4
3.75-3.923.8950.08112.374592125811790.9960.09393.7
3.92-4.113.8380.06315.154291120811180.9980.07192.5
4.11-4.333.8240.05517.894115114510760.9980.06294
4.33-4.593.7480.04720.233763107310040.9980.05493.6
4.59-4.913.7050.04422.03347910239390.9980.0591.8
4.91-5.33.6020.04422.4830339598420.9980.0587.8
5.3-5.813.6720.04722.3127728677550.9980.05487.1
5.81-6.53.8780.04125.3728397997320.9980.04691.6
6.5-7.53.8110.03629.0523937016280.9980.04289.6
7.5-9.193.8010.02833.1420265945330.9990.03289.7
9.19-12.993.7040.02634.6814414743890.9990.0382.1
12.99-19.724.0910.02936.726712641640.9990.03362.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.28 Å54.11 Å
Translation3.28 Å54.11 Å

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Processing

Software
NameVersionClassificationNB
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.5.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3lhk

3lhk


Resolution: 2.92→19.72 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.845 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.45 / SU Rfree Blow DPI: 0.38
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1596 10.12 %RANDOM
Rwork0.217 ---
obs0.22 15775 73.1 %-
Displacement parametersBiso max: 221.48 Å2 / Biso mean: 76.39 Å2 / Biso min: 6.55 Å2
Baniso -1Baniso -2Baniso -3
1-11.0692 Å20 Å2-0.6834 Å2
2---14.2129 Å20 Å2
3---3.1437 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 2.92→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3996 0 0 0 3996
Num. residues----574
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1263SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes632HARMONIC5
X-RAY DIFFRACTIONt_it4037HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion600SEMIHARMONIC5
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_contact4676SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4037HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5498HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion2.34
X-RAY DIFFRACTIONt_other_torsion20.13
LS refinement shellResolution: 2.92→3.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3427 57 9.79 %
Rwork0.2888 525 -
all0.294 582 -
obs--14.84 %
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)
15.80370.30430.81045.57272.18433.953-0.24410.51910.8272-0.2733-0.1212-0.0461-0.69580.07340.3653-0.09650.1122-0.0521-0.2508-0.024-0.108239.4361-9.990213.1255
210.1604-0.06615.23853.08390.33937.51340.44020.1442-0.7295-0.0116-0.16140.22990.7701-0.2542-0.27880.01750.0905-0.2619-0.4024-0.1729-0.201639.3589-31.208611.968
32.08650.5885-0.17126.1026-1.72333.1753-0.06180.2539-0.2607-1.5232-0.47370.22270.2522-0.18030.53550.43650.1921-0.2304-0.51780.07170.223221.597421.8667.6686
40.3753-1.11880.83265.03533.1362.510.07780.13360.4278-1.5232-0.78850.2227-1.34880.18040.71080.48480.2438-0.3957-0.60790.18160.086817.26542.17554.9294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A65 - 211
2X-RAY DIFFRACTION2{ B|* }B65 - 211
3X-RAY DIFFRACTION3{ C|* }C65 - 211
4X-RAY DIFFRACTION4{ D|* }D65 - 211

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