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- PDB-3wx4: CRYSTAL STRUCTURE of T4 PHAGE ARN PROTEIN -

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Basic information

Entry
Database: PDB / ID: 3wx4
TitleCRYSTAL STRUCTURE of T4 PHAGE ARN PROTEIN
ComponentsAnti-restriction endonuclease
KeywordsVIRAL PROTEIN / DNA MIMIC / GENE REGULATION
Function / homology
Function and homology information


symbiont-mediated evasion of host restriction-modification system / endonuclease activity / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response
Similarity search - Function
Alpha-Beta Plaits - #2770 / : / : / DNA Mimic Protein Arn / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Anti-restriction endonuclease
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHo, C.H. / Wang, H.C. / Ko, T.P. / Wang, A.H.J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The T4 phage DNA mimic protein Arn inhibits the DNA binding activity of the bacterial histone-like protein H-NS
Authors: Ho, C.H. / Wang, H.C. / Ko, T.P. / Chang, Y.C. / Wang, A.H.J.
History
DepositionJul 16, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-restriction endonuclease


Theoretical massNumber of molelcules
Total (without water)11,9821
Polymers11,9821
Non-polymers00
Water2,792155
1
A: Anti-restriction endonuclease

A: Anti-restriction endonuclease


Theoretical massNumber of molelcules
Total (without water)23,9632
Polymers23,9632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area2440 Å2
ΔGint-19 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.959, 81.959, 149.424
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

21A-548-

HOH

31A-635-

HOH

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Components

#1: Protein Anti-restriction endonuclease / Anti-rgl nuclease


Mass: 11981.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: arn, asiA.1, motA.-6 / Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39510
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 4.03 Å3/Da / Density % sol: 69.48 %
Crystal growpH: 8
Details: 50MM TRIS, 100MM NACL, 3.6M NA- FORMATE(RESERVOIR), 0.1M TRIS(RESERVOIR), PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9762
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2010 / Details: RH COATED MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 15419 / % possible obs: 99.4 % / Observed criterion σ(I): 5
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 6.15 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXSphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→24 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.232 737 RANDOM
Rwork0.208 --
obs0.208 14722 -
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms828 0 0 155 983
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.767
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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