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- PDB-3cae: Structure of NNQQNY as an insert in T7 endonuclease I -

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Basic information

Entry
Database: PDB / ID: 3cae
TitleStructure of NNQQNY as an insert in T7 endonuclease I
ComponentsEndonuclease I
KeywordsHYDROLASE / T7 endonuclease I / amyloid / steric zipper
Function / homology
Function and homology information


degradation of host chromosome by virus / deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / double-stranded DNA endonuclease activity / crossover junction DNA endonuclease activity / DNA integration / symbiont-mediated suppression of host gene expression / DNA binding
Similarity search - Function
Bacteriophage T7, Gp3, endodeoxynuclease I / Phage endonuclease I / Restriction Endonuclease - #30 / Restriction Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGuo, Z. / Eisenberg, D.
CitationJournal: Protein Sci. / Year: 2008
Title: The structure of a fibril-forming sequence, NNQQNY, in the context of a globular fold.
Authors: Guo, Z. / Eisenberg, D.
History
DepositionFeb 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 7, 2017Group: Database references / Source and taxonomy / Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Endonuclease I
B: Endonuclease I
C: Endonuclease I
D: Endonuclease I
E: Endonuclease I
F: Endonuclease I
G: Endonuclease I
H: Endonuclease I
I: Endonuclease I
J: Endonuclease I


Theoretical massNumber of molelcules
Total (without water)156,50810
Polymers156,50810
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.408, 140.343, 88.508
Angle α, β, γ (deg.)90.000, 93.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Endonuclease I / Endodeoxyribonuclease I / Endonuclease


Mass: 15650.829 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00641, deoxyribonuclease IV
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.5 Å3/Da / Density % sol: 64.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.6 M ammonium sulfate, 0.1 M sodium citrate, 2% dimethyl formamide, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2007
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→90 Å / Num. all: 43123 / Num. obs: 43123 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.052 / Χ2: 1 / Net I/σ(I): 14.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 4219 / Rsym value: 0.429 / Χ2: 1.006 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
BOSdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FZR, residues 18-43 of molecule A and residues 51-145 of molecule B

1fzr


Resolution: 3→90 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2165 5 %RANDOM
Rwork0.2405 ---
all-42973 --
obs-42973 99.4 %-
Solvent computationBsol: 62.292 Å2
Displacement parametersBiso mean: 86.205 Å2
Baniso -1Baniso -2Baniso -3
1-14.329 Å20 Å23.808 Å2
2---26.879 Å20 Å2
3---12.549 Å2
Refinement stepCycle: LAST / Resolution: 3→90 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11060 0 0 15 11075
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.349
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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