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- PDB-4m6f: Dimer of the G-Segment Invertase bound to a DNA substrate -

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Basic information

Entry
Database: PDB / ID: 4m6f
TitleDimer of the G-Segment Invertase bound to a DNA substrate
Components
  • (gix site analog) x 2
  • DNA-invertase
KeywordsHYDROLASE/DNA / Helix-turn-helix / catalytic domain / DNA Binding Domain / recombinase / HYDROLASE-DNA complex
Function / homology
Function and homology information


viral tropism switching / Ligases; Forming phosphoric-ester bonds / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / DNA strand exchange activity / ligase activity / DNA integration / host cell cytoplasm / hydrolase activity / symbiont entry into host cell / 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 ...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) / Serine recombinase gin
Similarity search - Component
Biological speciesEnterobacteria phage Mu (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.99 Å
AuthorsRitacco, C.J. / Wang, J. / Steitz, T.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Exploiting large non-isomorphous differences for phase determination of a G-segment invertase-DNA complex.
Authors: Ritacco, C.J. / Steitz, T.A. / Wang, J.
History
DepositionAug 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Database references / Source and taxonomy
Category: pdbx_entity_src_syn / reflns / struct_ref_seq_dif
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.3Feb 28, 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

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Assembly

Deposited unit
A: DNA-invertase
B: gix site analog
C: gix site analog


Theoretical massNumber of molelcules
Total (without water)32,4363
Polymers32,4363
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-36 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.800, 119.800, 343.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein DNA-invertase


Mass: 21714.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage Mu (virus) / References: UniProt: P03015
#2: DNA chain gix site analog


Mass: 5246.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain gix site analog


Mass: 5475.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3-5% Ammonium Sulfate 20% ethylene glycol 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-E11.0849
SYNCHROTRONNSLS X29A21.0849
SYNCHROTRONNSLS X29A31.14019
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJul 22, 2012
DECTRIS PILATUS 6M2PIXELDec 4, 2012
DECTRIS PILATUS 6M3PIXELAug 22, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
3GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.08491
21.140191
ReflectionResolution: 4.99→30 Å / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.5 % / Rmerge(I) obs: 0.111 / Rsym value: 12.05
Reflection shellResolution: 4.97→5.25 Å / % possible all: 94.6

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
CNS1.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 4.99→30 Å / σ(F): 1 / Stereochemistry target values: DEN
RfactorNum. reflectionSelection details
Rfree0.288 685 random
Rwork0.229 --
obs0.23 6853 -
Displacement parametersBiso mean: 335 Å2
Baniso -1Baniso -2Baniso -3
1-16.3 Å2--
2--16.3 Å2-
3----32.6 Å2
Refinement stepCycle: LAST / Resolution: 4.99→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 720 0 0 2196

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