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- PDB-5dcf: C-terminal domain of XerD recombinase in complex with gamma domai... -

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Basic information

Entry
Database: PDB / ID: 5dcf
TitleC-terminal domain of XerD recombinase in complex with gamma domain of FtsK
ComponentsTyrosine recombinase XerD,DNA translocase FtsK
KeywordsRECOMBINATION
Function / homology
Function and homology information


tyrosine-based site-specific recombinase activity / site-specific recombinase activity / plasmid recombination / double-stranded DNA helicase activity / resolution of DNA recombination intermediates / divisome complex / DNA transposition / Holliday junction resolvase complex / plasmid maintenance / septum digestion after cytokinesis ...tyrosine-based site-specific recombinase activity / site-specific recombinase activity / plasmid recombination / double-stranded DNA helicase activity / resolution of DNA recombination intermediates / divisome complex / DNA transposition / Holliday junction resolvase complex / plasmid maintenance / septum digestion after cytokinesis / DNA translocase activity / FtsZ-dependent cytokinesis / division septum assembly / response to osmotic stress / cellular response to antibiotic / cell division site / response to salt stress / chromosome segregation / sequence-specific DNA binding / cell cycle / cell division / positive regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / ATP binding / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tyrosine recombinase XerC / Tyrosine recombinase XerD / Tyrosine recombinase XerC/XerD / Phage integrase, N-terminal SAM-like domain / FtsK gamma domain / DNA translocase FtsK, 4TM region / FtsK alpha domain / Ftsk gamma domain / 4TM region of DNA translocase FtsK/SpoIIIE / FtsK alpha domain ...Tyrosine recombinase XerC / Tyrosine recombinase XerD / Tyrosine recombinase XerC/XerD / Phage integrase, N-terminal SAM-like domain / FtsK gamma domain / DNA translocase FtsK, 4TM region / FtsK alpha domain / Ftsk gamma domain / 4TM region of DNA translocase FtsK/SpoIIIE / FtsK alpha domain / Ftsk_gamma / Integrase, SAM-like, N-terminal / Intergrase catalytic core / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / hpI Integrase; Chain A / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family / Integrase, catalytic domain / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Tyrosine recombinase XerC / Tyrosine recombinase XerD / DNA translocase FtsK
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsKeller, A.N. / Xin, Y. / Lowe, J. / Grainge, I.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1005697 to I. Grainge Australia
CitationJournal: Sci Rep / Year: 2016
Title: Activation of Xer-recombination at dif: structural basis of the FtsK gamma-XerD interaction.
Authors: Keller, A.N. / Xin, Y. / Boer, S. / Reinhardt, J. / Baker, R. / Arciszewska, L.K. / Lewis, P.J. / Sherratt, D.J. / Lowe, J. / Grainge, I.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: diffrn_source / pdbx_audit_support ...diffrn_source / pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.country ..._diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.3Jan 8, 2020Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine recombinase XerD,DNA translocase FtsK


Theoretical massNumber of molelcules
Total (without water)30,7261
Polymers30,7261
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.451, 83.451, 88.672
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Tyrosine recombinase XerD,DNA translocase FtsK


Mass: 30725.848 Da / Num. of mol.: 1 / Fragment: unp residues 111-298 and 1261-1329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria), (gene. exp.) Escherichia coli (E. coli)
Strain: CFT073 / ATCC 700928 / UPEC, K12 / Gene: xerD, c3474, ftsK, b0890, JW0873 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A8P9, UniProt: P46889, UniProt: P0A8P6*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.9 Å3/Da / Density % sol: 57.6 % / Description: Trigonal bipyramidal
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: Bicine, PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→56.02 Å / Num. obs: 15676 / % possible obs: 100 % / Redundancy: 10.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.044 / Net I/σ(I): 62 / Num. measured all: 169816 / Scaling rejects: 3267
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.3811.21.73621737815520.5310.54100
8.91-56.0280.0521020.223202910.9980.0299.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.2.7data scaling
PHASERphasing
ARPmodel building
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A0P, 2J5P

1a0p

2j5p


Resolution: 2.3→36.135 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2289 781 5 %
Rwork0.1908 14853 -
obs0.1927 15634 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.04 Å2 / Biso mean: 74.4091 Å2 / Biso min: 30.9 Å2
Refinement stepCycle: final / Resolution: 2.3→36.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 0 61 1976
Biso mean---52.61 -
Num. residues----239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011951
X-RAY DIFFRACTIONf_angle_d1.1622639
X-RAY DIFFRACTIONf_chiral_restr0.049299
X-RAY DIFFRACTIONf_plane_restr0.006341
X-RAY DIFFRACTIONf_dihedral_angle_d15.243734
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3001-2.44420.28421250.27524612586
2.4442-2.63290.26451420.229524602602
2.6329-2.89770.25441060.220524882594
2.8977-3.31680.24591320.208724692601
3.3168-4.17780.20161390.189624762615
4.1778-36.13970.22141370.158824992636
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)
13.75630.4901-0.71623.4808-0.79484.2119-0.14270.01850.0186-0.36880.19960.12940.3058-0.2747-0.08830.4547-0.0243-0.00370.32560.00530.3948-13.471860.43893.3607
27.38191.16352.1463.82050.43095.1665-0.26050.7539-0.05-1.10620.0955-0.21320.43010.05530.2150.7857-0.06650.09780.480.00940.4832-5.101259.6716-6.291
33.30391.33820.18433.603-1.42363.6001-0.0651-0.7136-0.2207-0.0039-0.116-0.29030.48420.35850.18590.45390.0522-0.00790.41120.02230.3887-5.369651.765315.3015
41.49380.99670.21434.31910.24752.31710.0255-0.06830.24880.9585-0.1091-0.1218-1.06080.21650.05351.60380.0403-0.17720.9354-0.06471.0963-4.793378.028521.5434
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 102 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 124 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 182 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 276 )A0

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