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- PDB-5c35: Constitutively active Sin recombinase cataltyic domain - T77II100... -

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Basic information

Entry
Database: PDB / ID: 5c35
TitleConstitutively active Sin recombinase cataltyic domain - T77II100T/Q115R
ComponentsRecombinase Sin
KeywordsRECOMBINATION / Serine recombinase / site specific recombinase / Conformational flexibility
Function / homology
Function and homology information


transposition / DNA strand exchange activity / DNA integration / DNA binding
Similarity search - Function
Resolvase, N-terminal catalytic domain / 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 catalytic domain / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Recombinase Sin / Putative transposon Tn552 DNA-invertase bin3
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTrejo, C.S. / Rice, P.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)T32EB009412 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM086826 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM078450 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Snapshots of a molecular swivel in action
Authors: Trejo, C.S. / Rock, R.S. / Star, W.M. / Boocock, M.R. / Rice, P.A.
History
DepositionJun 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2018Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Recombinase Sin
B: Recombinase Sin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5814
Polymers30,3892
Non-polymers1922
Water362
1
A: Recombinase Sin
B: Recombinase Sin
hetero molecules

A: Recombinase Sin
B: Recombinase Sin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1628
Polymers60,7784
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5980 Å2
ΔGint-121 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.842, 73.842, 180.483
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

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Components

#1: Protein Recombinase Sin


Mass: 15194.476 Da / Num. of mol.: 2 / Fragment: UNP residues 1-128 / Mutation: R54E, T77I, I100T, Q115R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: sin, SAP013A_018, SAP095A_006, SAP096A_020 / Production host: Escherichia coli (E. coli) / References: UniProt: D2J612, UniProt: P20384*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10mM DTT, 500mM HEPES, pH 7.0, 0.96 M AmSO4, 8% PEG 400

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 12607 / % possible obs: 99.7 % / Redundancy: 17.3 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.028 / Rrim(I) all: 0.106 / Χ2: 1.993 / Net I/σ(I): 35.8 / Num. measured all: 211480
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Χ2% possible allRpim(I) allRrim(I) all
2.4-2.446.500.45070.1890.74396.5
2.4-2.446.65910.2140.73996.60.848
2.44-2.499.86130.3580.7721000.616
2.49-2.5413.36230.60.7551000.557
2.54-2.615.16080.6620.8141000.426
2.6-2.6615.86280.7440.8011000.399
2.66-2.7216.86160.8690.8311000.345
2.72-2.817.66240.9290.8061000.257
2.8-2.8818.60.8856180.9540.8391000.2090.91
2.88-2.9719.50.7136240.9660.8951000.1640.732
2.97-3.0819.80.5486320.9810.9471000.1250.563
3.08-3.220.30.4216330.990.9721000.0950.432
3.2-3.3520.30.2826230.9911.1431000.0640.29
3.35-3.5320.20.2196330.9961.2631000.0490.225
3.53-3.75200.1486470.9981.5661000.0340.152
3.75-4.0320.10.126390.9981.8711000.0270.124
4.03-4.4420.10.096490.9992.6421000.0210.092
4.44-5.0819.50.0856530.9993.6961000.020.088
5.08-6.418.60.0876880.9994.8611000.020.089
6.4-5015.90.0737580.9989.03898.70.0190.076

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX(phenix.refine: dev_1951)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIX(phenix.refine: dev_1951)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3pkz

3pkz


Resolution: 2.4→36.172 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3353 2115 9.95 %
Rwork0.3159 --
obs0.3179 12607 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 406.17 Å2 / Biso mean: 146.8307 Å2 / Biso min: 55.84 Å2
Refinement stepCycle: final / Resolution: 2.4→36.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 10 2 2005
Biso mean--141.59 86.11 -
Num. residues----246
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)
10.2246-0.06360.00630.1523-0.02060.32280.00560.4569-0.142-0.87020.0131-0.2693-0.05610.217501.0811-0.44780.02990.7955-0.10410.758716.4209-16.3453-18.7501
21.1172-1.2469-0.32931.43490.38920.1154-0.3723-0.6013-0.34270.37750.01691.22210.0501-0.5593-0.07310.8142-0.4489-0.03191.05330.03720.87887.9026-15.5366-9.9427
30.1165-0.03430.04130.28420.10940.08330.1493-0.0007-0.0408-0.09110.0832-0.0999-0.04840.00360.21470.8602-0.41840.17240.6962-0.08730.950220.3681-8.4659-14.9199
40.0339-0.0395-0.04930.06530.11060.231-0.0181-0.23150.50930.1562-0.29260.2245-0.618-0.3242-0.00510.5346-0.2690.03490.9095-0.02630.857612.3621-4.5301-6.2462
50.0250.0393-0.00750.0524-0.01140.00710.2481-0.3298-0.47840.52960.04680.23340.7517-0.200800.7334-0.21330.07371.2190.00790.900816.7434-15.6406-4.6078
60.198-0.1705-0.23170.23490.19880.4669-0.5045-0.9613-0.05030.62870.7125-1.40050.75880.81580.02780.7411-0.14440.08511.0891-0.24980.968924.1255-7.6405-1.2839
70.0727-0.0530.00050.17290.00710.0077-0.2958-0.0481-0.13180.39090.07320.14870.18660.0983-0.34241.17682.5368-0.51951.81640.5080.929442.7217-12.106123.2527
8-0.0088-0.0003-0.0057-0.0046-0.00520.0023-0.01940.37590.0064-0.0041-0.0055-0.03730.00450.07701.36560.8252-0.96451.4396-0.12241.312849.31192.283620.0715
90.0310.04-0.01960.033-0.02030.0181-0.61840.1541-0.0448-0.0138-0.1881-0.4036-0.1188-0.023-00.87470.8322-0.12932.5948-0.03531.481853.6505-11.383113.2824
100.1148-0.1027-0.12230.29670.17750.1844-0.1228-0.21340.09990.4060.559-0.05610.12710.07110.2463-0.15521.02860.07492.66230.59911.232444.1444-4.149311.1231
11-0.0014-0.0018-0.0002-0.01370.00560.0097-0.3363-0.4199-0.43360.17160.54370.51570.81770.284301.10150.49260.0441.91810.39841.150937.472-13.83855.9232
120.03870.0753-0.00350.0841-0.04390.10040.060.23340.29820.10170.03080.1151-0.18440.27750.00180.70590.2241-0.02641.47050.56171.142835.2139-2.39774.8956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:43 )A1 - 43
2X-RAY DIFFRACTION2( CHAIN A AND RESID 44:61 )A44 - 61
3X-RAY DIFFRACTION3( CHAIN A AND RESID 62:70 )A62 - 70
4X-RAY DIFFRACTION4( CHAIN A AND RESID 71:83 )A71 - 83
5X-RAY DIFFRACTION5( CHAIN A AND RESID 84:93 )A84 - 93
6X-RAY DIFFRACTION6( CHAIN A AND RESID 94:124 )A94 - 124
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1:33 )B1 - 33
8X-RAY DIFFRACTION8( CHAIN B AND RESID 34:43 )B34 - 43
9X-RAY DIFFRACTION9( CHAIN B AND RESID 44:57 )B44 - 57
10X-RAY DIFFRACTION10( CHAIN B AND RESID 58:83 )B58 - 83
11X-RAY DIFFRACTION11( CHAIN B AND RESID 84:102 )B84 - 102
12X-RAY DIFFRACTION12( CHAIN B AND RESID 103:124 )B103 - 124

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