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- PDB-5cy2: Tn3 resolvase - site III complex crystal form II -

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Basic information

Entry
Database: PDB / ID: 5cy2
TitleTn3 resolvase - site III complex crystal form II
Components
  • (DNA (27-MER)) x 2
  • Transposon Tn3 resolvase
Keywordsrecombination/DNA / DNA recombinase repressor DNA binding protein phosphotransferase / recombination-DNA complex
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA binding
Similarity search - Function
Site-specific recombinases signature 2. / Resolvase, HTH domain / Helix-turn-helix domain of resolvase / 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 / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Transposon Tn3 resolvase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsMontano, P.S. / Rice, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM086826 United States
CitationJournal: To Be Published
Title: Structures of resolvase - accessory site complexes
Authors: Montano, S.P. / Rice, P.A.
History
DepositionJul 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 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: Transposon Tn3 resolvase
B: Transposon Tn3 resolvase
C: DNA (27-MER)
D: DNA (27-MER)
E: Transposon Tn3 resolvase
F: Transposon Tn3 resolvase
G: DNA (27-MER)
H: DNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)119,3828
Polymers119,3828
Non-polymers00
Water0
1
A: Transposon Tn3 resolvase
B: Transposon Tn3 resolvase
C: DNA (27-MER)
D: DNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)59,6914
Polymers59,6914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11190 Å2
ΔGint-46 kcal/mol
Surface area26190 Å2
MethodPISA
2
E: Transposon Tn3 resolvase
F: Transposon Tn3 resolvase
G: DNA (27-MER)
H: DNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)59,6914
Polymers59,6914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-47 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.900, 151.920, 106.140
Angle α, β, γ (deg.)90.00, 99.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Transposon Tn3 resolvase


Mass: 21551.609 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tnpR / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADI2
#2: DNA chain DNA (27-MER)


Mass: 8320.393 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (27-MER)


Mass: 8267.387 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.82 Å3/Da / Density % sol: 74.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: complex + well mixed 1:1 complex: 3mg/ml in 25mM tris pH 7.5 and 0.14M (NH4)2SO4 well: 16% PEG3350, 0.2M ammonium flouride cryoprotectant: added 20% ethylene glycol

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: flash-frozen crystal
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 4→100 Å / Num. all: 19099 / Num. obs: 19099 / % possible obs: 99.5 % / Redundancy: 3.5 % / Net I/σ(I): 22.9
Reflection shellResolution: 4→4.07 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIXdev_2067refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1000212338

Resolution: 4→49.247 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 968 5.08 %
Rwork0.2072 --
obs0.2094 19059 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4→49.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5590 2202 0 0 7792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018084
X-RAY DIFFRACTIONf_angle_d1.0911307
X-RAY DIFFRACTIONf_dihedral_angle_d18.0864569
X-RAY DIFFRACTIONf_chiral_restr0.0551310
X-RAY DIFFRACTIONf_plane_restr0.0051081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.21080.36151420.33082482X-RAY DIFFRACTION96
4.2108-4.47450.32871340.28772549X-RAY DIFFRACTION100
4.4745-4.81970.33161380.2592601X-RAY DIFFRACTION100
4.8197-5.30420.26851130.25472618X-RAY DIFFRACTION100
5.3042-6.07050.26661420.23192613X-RAY DIFFRACTION100
6.0705-7.64360.2821470.24872593X-RAY DIFFRACTION100
7.6436-49.25090.19821520.14862635X-RAY DIFFRACTION100
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)
110.8417-7.5848-3.191212.21322.7786.7151-0.05580.58240.09420.3997-0.00971.10150.1517-0.5801-0.00031.904-0.0512-0.09442.0320.41172.03394.8344-0.4254-18.7699
23.06550.16631.13774.12634.14753.69740.1424-1.1459-3.5134-0.2210.6040.87492.01540.29970.00442.69780.4860.32683.18041.28223.295619.4591-30.659212.0687
30.6734-3.9031.252911.1371.93034.8947-0.36580.7149-2.1586-0.2447-0.6432-0.19660.8672-0.20810.00222.54910.028-0.04172.4920.02733.263315.3595-28.0442-27.8638
410.5380.136-0.04471.86631.53910.6014-0.3083-0.88360.8851-0.29470.4942-0.1465-0.98630.37080.00042.454-0.1291-0.07362.23820.26072.010435.52332.9689-4.5911
53.634-1.99821.62110.97760.61213.7496-0.0682-1.7665-1.73571.3960.4194-0.41120.1204-0.96860.00852.31720.46150.09673.51921.13352.55217.7422-20.641418.0855
60.33051.6483-0.6842.38390.5652-0.7948-0.9120.75260.1685-0.43660.4752-0.25990.03521.0880.00062.1276-0.176-0.05942.58080.532.041340.7197-0.6863-9.9872
73.2693-1.1265-2.37220.14770.85470.2187-0.3832-0.4507-0.2401-0.9273-0.2805-0.3110.0470.70420.0012.2162-0.1197-0.14332.48530.54712.344944.2181.2101-8.6479
81.2523-2.0349-0.97733.02070.4104-0.1517-0.0902-1.8801-0.31650.8562-0.11920.65050.13250.98540.00172.48580.05480.22983.29791.0582.198917.016-17.500715.8735
98.7729-3.18611.300311.3258-1.956410.56170.13490.02790.19331.1888-0.74550.0387-0.94630.3234-0.00192.13710.0678-0.24021.99320.40052.103-20.8121.7422-21.3801
102.6624-0.41182.18447.88592.86236.2614-0.3537-0.80731.02381.2312-0.63140.6748-0.7743-0.46960.00192.27690.12220.21292.04560.46983.0091-66.600624.1293-15.8761
116.12421.9387-2.61816.39443.94212.6479-0.2481-1.22121.32721.0928-0.20890.2463-0.5186-0.25080.00153.520.5253-0.40372.501-0.08583.8704-34.256146.9509-8.6458
123.897-3.24512.94714.7906-1.88266.97280.45081.922-0.3212-0.70760.3621-0.4408-0.07180.231-0.00292.0873-0.11880.03213.3610.56852.2579-41.083825.9198-47.4609
131.1549-0.8369-1.08661.1422-0.3393-1.7722-0.20140.5617-0.0402-0.1831-0.49370.29660.5976-0.6405-0.00052.3205-0.06920.06142.6360.64792.3967-64.840613.951-21.8532
14-1.0374-0.56791.625-0.16331.37673.35950.82721.98390.9839-0.13490.90340.5516-0.8025-1.5571-0.00292.42120.0690.21083.39511.34452.7251-40.987534.2427-48.7114
151.76450.41443.071.9564-0.54061.94860.3592.23661.3168-0.9411-0.2839-0.0797-0.37180.65580.00222.64790.28130.0212.96681.01472.4798-42.093334.1831-52.6409
163.2761-4.79370.59813.64140.2174.0113-0.20812.14980.76090.42710.6611.01620.0833-0.45170.00032.1293-0.12220.17232.27190.56592.1777-61.160613.3476-23.0498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 136 through 186 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 103 )
4X-RAY DIFFRACTION4chain 'B' and (resid 104 through 185 )
5X-RAY DIFFRACTION5chain 'C' and (resid 2 through 15 )
6X-RAY DIFFRACTION6chain 'C' and (resid 16 through 28 )
7X-RAY DIFFRACTION7chain 'D' and (resid 2 through 16 )
8X-RAY DIFFRACTION8chain 'D' and (resid 17 through 28 )
9X-RAY DIFFRACTION9chain 'E' and (resid 1 through 128 )
10X-RAY DIFFRACTION10chain 'E' and (resid 136 through 186 )
11X-RAY DIFFRACTION11chain 'F' and (resid 1 through 103 )
12X-RAY DIFFRACTION12chain 'F' and (resid 104 through 185 )
13X-RAY DIFFRACTION13chain 'G' and (resid 2 through 15 )
14X-RAY DIFFRACTION14chain 'G' and (resid 16 through 28 )
15X-RAY DIFFRACTION15chain 'H' and (resid 2 through 16 )
16X-RAY DIFFRACTION16chain 'H' and (resid 17 through 28 )

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