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- PDB-5vfz: Integrase from mycobacterium phage Brujita -

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Basic information

Entry
Database: PDB / ID: 5vfz
TitleIntegrase from mycobacterium phage Brujita
ComponentsGp33
KeywordsDNA BINDING PROTEIN / Bacteriophage / Brujita / DNA-binding / Integrase
Function / homology
Function and homology information


DNA integration / transferase activity / DNA recombination / DNA binding
Similarity search - Function
: / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core
Similarity search - Domain/homology
ACETATE ION / Integrase
Similarity search - Component
Biological speciesMycobacterium phage Brujita (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.847 Å
AuthorsVanDemark, A.P. / Lunt, B. / Hatfull, G.F.
CitationJournal: To Be Published
Title: Integrase from mycobacterium phage Brujita
Authors: Lunt, B. / VanDemark, A.P. / Hatfull, G.F.
History
DepositionApr 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support / Item: _citation.title
Revision 1.2Mar 13, 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: Gp33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3445
Polymers36,1101
Non-polymers2334
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.213, 50.050, 60.679
Angle α, β, γ (deg.)90.00, 115.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Gp33


Mass: 36110.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium phage Brujita (virus) / Gene: 33, BRUJITA_33 / Production host: Escherichia coli (E. coli) / References: UniProt: B5U3A1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris pH 7.5 5% PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.847→50 Å / Num. obs: 31131 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.024 / Net I/σ(I): 40.3

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Processing

Software
NameVersionClassification
PHENIX(dev_2219: ???)refinement
HKL-2000data scaling
HKL-2000data processing
PHENIXphasing
RefinementResolution: 1.847→21.699 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.43
RfactorNum. reflection% reflection
Rfree0.1818 1007 3.23 %
Rwork0.1635 --
obs0.1641 31131 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.847→21.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2309 0 15 152 2476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062393
X-RAY DIFFRACTIONf_angle_d0.6573234
X-RAY DIFFRACTIONf_dihedral_angle_d11.2781425
X-RAY DIFFRACTIONf_chiral_restr0.04347
X-RAY DIFFRACTIONf_plane_restr0.004419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.847-1.94430.29111440.25424189X-RAY DIFFRACTION98
1.9443-2.0660.26711480.20724289X-RAY DIFFRACTION100
2.066-2.22540.21341430.16824292X-RAY DIFFRACTION100
2.2254-2.44910.19291430.16054292X-RAY DIFFRACTION100
2.4491-2.80280.14981460.15754308X-RAY DIFFRACTION100
2.8028-3.52880.17731390.16894333X-RAY DIFFRACTION100
3.5288-21.70010.16661440.14814421X-RAY DIFFRACTION100

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