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- PDB-4j2n: Crystal Structure of mycobacteriophage Pukovnik Xis -

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Basic information

Entry
Database: PDB / ID: 4j2n
TitleCrystal Structure of mycobacteriophage Pukovnik Xis
ComponentsGp37
KeywordsVIRAL PROTEIN / Winged-Helix / Doman Swap / Filament
Function / homologySinI-like, DNA-binding domain / Helix-turn-helix domain, group 17 / Helix-turn-helix domain / Putative DNA-binding domain superfamily / DNA binding / Excise
Function and homology information
Biological speciesMycobacterium phage Pukovnik (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.348 Å
AuthorsHoma, N.J. / Amrich, C.G. / Heroux, A. / VanDemark, A.P.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: The Structure of Xis Reveals the Basis for Filament Formation and Insight into DNA Bending within a Mycobacteriophage Intasome.
Authors: Singh, S. / Plaks, J.G. / Homa, N.J. / Amrich, C.G. / Heroux, A. / Hatfull, G.F. / Vandemark, A.P.
History
DepositionFeb 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gp37
B: Gp37
D: Gp37
C: Gp37
E: Gp37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,80213
Polymers32,0335
Non-polymers7698
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.423, 129.985, 92.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Gp37


Mass: 6406.617 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium phage Pukovnik (virus) / Strain: Pukovnik / Gene: 37, Pukovnik_37, XIS / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+RILP / References: UniProt: B3VGI6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.63 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8
Details: ammonium sulfate, PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E DW11.5418
SYNCHROTRONNSLS X2520.9791
Detector
TypeIDDetectorDate
RIGAKU SATURN 9441CCDJul 15, 2009
ADSC QUANTUM 42CCDOct 2, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2Si-111 double crystal
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97911
ReflectionResolution: 2.35→90 Å / Num. all: 22860 / Num. obs: 22815 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Biso Wilson estimate: 45.18 Å2
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1127 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.1_357phasing
RefinementMethod to determine structure: SAD / Resolution: 2.348→35.921 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.7672 / SU ML: 0.35 / σ(F): 0.03 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1788 8.81 %RANDOM
Rwork0.2257 ---
all0.264 22795 --
obs0.2294 20286 88.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.428 Å2 / ksol: 0.392 e/Å3
Displacement parametersBiso max: 112.21 Å2 / Biso mean: 54.6141 Å2 / Biso min: 34.42 Å2
Baniso -1Baniso -2Baniso -3
1-24.4775 Å2-0 Å2-0 Å2
2---8.6062 Å20 Å2
3----15.8713 Å2
Refinement stepCycle: LAST / Resolution: 2.348→35.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 40 140 2293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072179
X-RAY DIFFRACTIONf_angle_d0.9842944
X-RAY DIFFRACTIONf_chiral_restr0.055343
X-RAY DIFFRACTIONf_plane_restr0.005370
X-RAY DIFFRACTIONf_dihedral_angle_d14.174864
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3477-2.43160.35481590.28861530168975
2.4316-2.52890.31381600.26261640180080
2.5289-2.6440.3111630.25611611177479
2.644-2.78330.25721710.24281734190585
2.7833-2.95760.31361740.2361821199588
2.9576-3.18580.30011860.25351887207391
3.1858-3.50620.28381910.22471997218897
3.5062-4.0130.26691950.21682069226498
4.013-5.05370.22941910.18092062225398
5.0537-35.92560.22711980.21522147234597

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