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- PDB-5cy1: Tn3 resolvase - site III complex crystal form I -

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Basic information

Entry
Database: PDB / ID: 5cy1
TitleTn3 resolvase - site III complex crystal form I
Components
  • (DNA (30-MER)) x 2
  • Transposon Tn3 resolvase
KeywordsHYDROLASE / LIGASE/DNA / DNA recombinase repressor DNA binding protein / LIGASE-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 / MIR / Resolution: 3.4 Å
AuthorsMontano, S.P. / 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: Tn3 resolvase - accessory site complexes: DNA geometry dictates complex geometry
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 (30-MER)
D: DNA (30-MER)


Theoretical massNumber of molelcules
Total (without water)61,5454
Polymers61,5454
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-44 kcal/mol
Surface area27810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.313, 77.313, 272.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Transposon Tn3 resolvase


Mass: 21551.609 Da / Num. of mol.: 2
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 (30-MER)


Mass: 9233.959 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (30-MER)


Mass: 9207.995 Da / Num. of mol.: 1 / 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: 3.31 Å3/Da / Density % sol: 62.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: well + complex mixed 1:1 complex: 6mg/ml in 25mM tris pH 7.5, 0.18M (NH4)2SO4 well: 20% PEG3350, 0.2M sodium malonate pH 7.0 microseeding required cryoprotectant: crop conditions plus 20% PEG400 and 10% glycerol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 3.4→100 Å / Num. obs: 12184 / % possible obs: 99.9 % / Redundancy: 7.6 % / Net I/σ(I): 34.2
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIXdev_2067refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
SOLVEphasing
Cootmodel building
RefinementMethod to determine structure: MIR / Resolution: 3.4→29.427 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2919 575 4.76 %
Rwork0.2485 --
obs0.2506 12089 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→29.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 1224 0 0 4072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034234
X-RAY DIFFRACTIONf_angle_d0.5385939
X-RAY DIFFRACTIONf_dihedral_angle_d18.0082381
X-RAY DIFFRACTIONf_chiral_restr0.028686
X-RAY DIFFRACTIONf_plane_restr0.001557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.74160.35461440.35182779X-RAY DIFFRACTION100
3.7416-4.28150.27331350.29352829X-RAY DIFFRACTION100
4.2815-5.38890.32461500.29432848X-RAY DIFFRACTION100
5.3889-29.42810.27591460.21053058X-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)
19.17330.9235-2.37879.2657-0.0626.86220.4478-0.01410.50650.3329-0.26960.787-0.61140.2694-0.00011.4335-0.4044-0.21751.198-0.00551.145834.232526.190373.007
21.9953-6.7812-8.64789.30682.003621.45123.59523.1056-3.80613.5565-0.8581-2.04011.72455.41022.1671-1.4693-0.56383.7139-0.01391.632529.320715.997550.9069
31.43440.4679-0.88342.4168-0.61981.5622-1.19161.5690.2865-1.62960.83920.4692-0.5324-0.01220.00011.8073-0.51250.02682.06580.0351.253515.2883-1.359940.4905
41.4294-0.6451-1.06191.7672.05142.440.60510.7459-1.0187-0.5032-0.38090.20772.41960.0356-0.00012.4944-0.26050.03972.2137-0.16112.418852.76748.927955.0472
52.48661.4205-2.12161.5805-0.69161.7847-0.0805-0.2582-0.20740.2796-0.095-0.5330.3017-0.0177-0.00031.4549-0.2485-0.31061.33680.03761.493523.0661-3.638981.7138
61.2776-0.0066-1.6233.2106-0.87032.1493-0.52920.04450.8493-0.4277-0.2905-0.0276-0.6327-1.2340.00031.8734-0.3173-0.35891.6745-0.05981.63765.67432.178647.4965
70.03460.05350.10650.24530.32160.2117-0.1259-0.14280.12031.4214-0.5427-1.53030.26751.4441-0.00111.8847-0.1443-0.47811.87740.59992.096230.9325-9.64183.4881
81.3095-0.7724-0.24840.6363-0.61351.1143-0.0641-0.16380.6195-0.4071-0.3895-0.97381.2010.592-0.00191.7564-0.265-0.47171.70060.45212.045529.264-12.443484.231
91.862.4042-0.31292.8373-0.50440.2329-0.85370.1756-0.5127-0.56330.5705-0.2487-1.095-0.1274-0.00011.5734-0.3727-0.36641.64960.02011.4715.89764.807148.911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 128 )
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 186 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 103 )
5X-RAY DIFFRACTION5chain 'B' and (resid 104 through 185 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 15 )
7X-RAY DIFFRACTION7chain 'C' and (resid 16 through 30 )
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 16 )
9X-RAY DIFFRACTION9chain 'D' and (resid 17 through 30 )

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