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- PDB-5u96: Crystal structure of the coiled-coil domain from Listeria Innocua... -

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Basic information

Entry
Database: PDB / ID: 5u96
TitleCrystal structure of the coiled-coil domain from Listeria Innocua (Tetragonal Form)
ComponentsPutative integrase
KeywordsRECOMBINATION / site-specific recombination / coiled-coil
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA binding / metal ion binding
Similarity search - Function
Recombinase zinc beta ribbon domain / Recombinase / Recombinase zinc beta ribbon domain / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / Recombinase, conserved site / Site-specific recombinases active site. / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain ...Recombinase zinc beta ribbon domain / Recombinase / Recombinase zinc beta ribbon domain / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / 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
Similarity search - Domain/homology
Integrase [Bacteriophage A118]
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGupta, K. / Van Duyne, G.D. / Sharp, R. / Yuan, J.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 R01 GM108751 03 United States
Citation
Journal: Nucleic Acids Res. / Year: 2017
Title: Coiled-coil interactions mediate serine integrase directionality.
Authors: Gupta, K. / Sharp, R. / Yuan, J.B. / Li, H. / Van Duyne, G.D.
#1: Journal: Nucleic Acids Res. / Year: 2013
Title: Attachment site recognition and regulation of directionality by the serine integrases.
Authors: Rutherford, K. / Yuan, P. / Perry, K. / Sharp, R. / Van Duyne, G.D.
History
DepositionDec 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: Putative integrase
B: Putative integrase
C: Putative integrase
D: Putative integrase
E: Putative integrase
F: Putative integrase
G: Putative integrase
H: Putative integrase


Theoretical massNumber of molelcules
Total (without water)48,5988
Polymers48,5988
Non-polymers00
Water15,241846
1
A: Putative integrase
B: Putative integrase


Theoretical massNumber of molelcules
Total (without water)12,1502
Polymers12,1502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-6 kcal/mol
Surface area7230 Å2
MethodPISA
2
C: Putative integrase
D: Putative integrase


Theoretical massNumber of molelcules
Total (without water)12,1502
Polymers12,1502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-6 kcal/mol
Surface area6820 Å2
MethodPISA
3
E: Putative integrase
F: Putative integrase


Theoretical massNumber of molelcules
Total (without water)12,1502
Polymers12,1502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-6 kcal/mol
Surface area6890 Å2
MethodPISA
4
G: Putative integrase
H: Putative integrase


Theoretical massNumber of molelcules
Total (without water)12,1502
Polymers12,1502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-10 kcal/mol
Surface area6930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.160, 97.160, 52.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Putative integrase


Mass: 6074.780 Da / Num. of mol.: 8 / Fragment: Coiled-coil domain (UNP residues 350-400)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: int / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q928V6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 846 / 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: 2.32 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0 M ammonium sulfate, 100 mM HEPES pH 7.5, and 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→35.7 Å / Num. obs: 36018 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.019 / Net I/σ(I): 21.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KIS

4kis


Resolution: 1.95→35.688 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.29 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 1996 5.54 %Random Selection
Rwork0.2263 ---
obs0.2382 36018 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→35.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 0 846 4031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033225
X-RAY DIFFRACTIONf_angle_d0.5574314
X-RAY DIFFRACTIONf_dihedral_angle_d16.8051246
X-RAY DIFFRACTIONf_chiral_restr0.024461
X-RAY DIFFRACTIONf_plane_restr0.001556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9506-1.99930.37891410.35372406X-RAY DIFFRACTION94
1.9993-2.05340.3381410.33612407X-RAY DIFFRACTION94
2.0534-2.11380.36241400.33132436X-RAY DIFFRACTION95
2.1138-2.1820.32391410.30772404X-RAY DIFFRACTION94
2.182-2.260.32351480.3152438X-RAY DIFFRACTION94
2.26-2.35040.29041440.30112394X-RAY DIFFRACTION94
2.3504-2.45740.28371390.2812413X-RAY DIFFRACTION95
2.4574-2.58690.24161410.26442399X-RAY DIFFRACTION94
2.5869-2.74890.30821420.25422450X-RAY DIFFRACTION95
2.7489-2.96110.21831410.24062394X-RAY DIFFRACTION94
2.9611-3.25880.26511440.23342471X-RAY DIFFRACTION94
3.2588-3.72990.20181410.21172434X-RAY DIFFRACTION94
3.7299-4.69740.18621410.17752443X-RAY DIFFRACTION94
4.6974-34.35660.23881520.22912501X-RAY DIFFRACTION93

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