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

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Basic information

Entry
Database: PDB / ID: 5uae
TitleCrystal structure of the coiled-coil domain from Listeria Innocua Phage Integrase (Trigonal 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. ...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
CITRATE ANION / Integrase [Bacteriophage A118]
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGupta, K. / Sharp, R. / Yuan, J.B. / Van Duyne, G.D.
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 19, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4029
Polymers29,4574
Non-polymers9465
Water4,486249
1
A: Putative integrase
B: Putative integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1074
Polymers14,7282
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-7 kcal/mol
Surface area8510 Å2
MethodPISA
2
C: Putative integrase
D: Putative integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2965
Polymers14,7282
Non-polymers5673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-7 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.432, 75.432, 103.061
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Putative integrase


Mass: 7364.188 Da / Num. of mol.: 4 / Fragment: Coiled Coil Domain (UNP residues 344-405)
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: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 5.75 Å3/Da / Density % sol: 78.6 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.8-1.2 M Na Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→37.716 Å / Num. obs: 69598 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 91.1 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.3
Reflection shellResolution: 2.75→2.848 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.8 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KIS

4kis


Resolution: 2.75→37.716 Å / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 28.78 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 1704 10.01 %Random Selection
Rwork0.2158 ---
obs0.2213 17022 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→37.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 65 249 2286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022052
X-RAY DIFFRACTIONf_angle_d0.5852749
X-RAY DIFFRACTIONf_dihedral_angle_d15.816809
X-RAY DIFFRACTIONf_chiral_restr0.021285
X-RAY DIFFRACTIONf_plane_restr0.001366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7514-2.83240.43461490.39371291X-RAY DIFFRACTION89
2.8324-2.92370.36231340.38571284X-RAY DIFFRACTION90
2.9237-3.02820.43061440.3631290X-RAY DIFFRACTION90
3.0282-3.14930.36161460.33281245X-RAY DIFFRACTION89
3.1493-3.29250.26581380.30661269X-RAY DIFFRACTION90
3.2925-3.46590.28591490.27461282X-RAY DIFFRACTION89
3.4659-3.68280.28581400.24241257X-RAY DIFFRACTION90
3.6828-3.96670.26631430.22541300X-RAY DIFFRACTION90
3.9667-4.3650.22651350.19121249X-RAY DIFFRACTION90
4.365-4.99470.21961510.1751268X-RAY DIFFRACTION89
4.9947-6.28550.29861270.2371288X-RAY DIFFRACTION91
6.2855-32.66530.19861440.15421268X-RAY DIFFRACTION89

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