- PDB-4zwq: Crystal Structure of the Bacteriophage T4 recombination mediator ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4zwq
Title
Crystal Structure of the Bacteriophage T4 recombination mediator protein UvsY, Lattice Type I
Components
Recombination protein uvsY
Keywords
VIRAL PROTEIN / recombination / DNA binding / homo-heptamer / asymmetry / alpha barrel
Function / homology
Recombination, repair and ssDNA binding protein UvsY / Recombination, repair and ssDNA binding protein UvsY / DNA biosynthetic process / DNA recombination / DNA binding / Recombination protein uvsY
A: Recombination protein uvsY B: Recombination protein uvsY C: Recombination protein uvsY D: Recombination protein uvsY E: Recombination protein uvsY F: Recombination protein uvsY G: Recombination protein uvsY
Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA
Dom-ID
Beg auth comp-ID
Beg label comp-ID
Selection details
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
HIS
HIS
chainA
A
A
0 - 135
20 - 155
2
MET
MET
chainB
B
B
1 - 135
21 - 155
3
ARG
ARG
chainC
C
C
2 - 135
22 - 155
4
MET
MET
chainD
D
D
1 - 135
21 - 155
5
MET
MET
chainE
E
E
1 - 135
21 - 155
6
ARG
ARG
chainF
F
F
2 - 135
22 - 155
7
GLU
GLU
chainG
G
G
4 - 135
24 - 155
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Components
#1: Protein
RecombinationproteinuvsY
Mass: 18036.621 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: uvsY / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04537
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.2 Å3/Da / Density % sol: 61.56 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1:1 UvsY (12.5 mg/mL in 0.5 M sodium chloride, 15 mM HEPES, pH 8.2, 2 mM DTT) to 1.8 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 2% 1,6-hexanediol, sample subjected to reductive alkylation with ...Details: 1:1 UvsY (12.5 mg/mL in 0.5 M sodium chloride, 15 mM HEPES, pH 8.2, 2 mM DTT) to 1.8 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 2% 1,6-hexanediol, sample subjected to reductive alkylation with formaldehyde prior to crystallization
Resolution: 2.351→46.727 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.59 / Stereochemistry target values: TWIN_LSQ_F Details: THE X-RAY DIFFRACTION DATA EXHIBITED STRONG ANISOTROPY. REFINEMENT WAS PERFORMED AGAINST ELLIPTICALLY TRUNCATED DATA (RESOLUTION LIMITS OF 1/3.0, 1/3.0, AND 1/2.3 A IN A*, B*, C*, ...Details: THE X-RAY DIFFRACTION DATA EXHIBITED STRONG ANISOTROPY. REFINEMENT WAS PERFORMED AGAINST ELLIPTICALLY TRUNCATED DATA (RESOLUTION LIMITS OF 1/3.0, 1/3.0, AND 1/2.3 A IN A*, B*, C*, RESPECTIVELY) CORRECTED BY ANISOTROPIC SCALE FACTORS AND AN ISOTROPIC B OF -34.50 A2 USING THE UCLA DIFFRACTION ANISOTROPY SERVER (STRONG ET AL., 2006).
Rfactor
Num. reflection
% reflection
Rfree
0.2542
2167
4.99 %
Rwork
0.2218
41283
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obs
0.2232
43451
64.24 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL