- PDB-4ezd: Crystal Structure of the UT-B Urea Transporter from Bos Taurus Bo... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4ezd
Title
Crystal Structure of the UT-B Urea Transporter from Bos Taurus Bound to Selenourea
Components
Urea transporter 1
Keywords
TRANSPORT PROTEIN / Membrane protein / channel / urea transport / slc14 / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS
Function / homology
Function and homology information
Transport of bile salts and organic acids, metal ions and amine compounds / urea channel activity / urea transmembrane transport / urea transmembrane transporter activity / water transmembrane transporter activity / establishment of localization in cell / basolateral plasma membrane / identical protein binding / plasma membrane Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
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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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 25% PEG 400, 50 mM sodium sulfate, 50 mM lithium sulfate, 0.2 mM DDAO, 100 mM Tris pH 8.0-8.5, 20 mM selenourea, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9788 Å / Relative weight: 1
Reflection
Resolution: 2.5→50 Å / Num. obs: 56923 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.168 / Χ2: 1.025 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
2.5-2.54
6.7
0.921
2788
0.94
1
100
2.54-2.59
6.8
0.87
2884
0.943
1
100
2.59-2.64
6.9
0.854
2806
1.016
1
100
2.64-2.69
7
0.726
2816
0.964
1
100
2.69-2.75
7.1
0.63
2855
0.98
1
100
2.75-2.82
7.1
0.538
2838
1.021
1
100
2.82-2.89
7.1
0.463
2862
1.081
1
100
2.89-2.96
7.2
0.438
2827
1.062
1
100
2.96-3.05
7.2
0.406
2811
1.026
1
100
3.05-3.15
7.2
0.345
2850
1.123
1
100
3.15-3.26
7.1
0.283
2866
1.065
1
100
3.26-3.39
7.1
0.229
2822
1.061
1
100
3.39-3.55
7.1
0.181
2843
1.072
1
100
3.55-3.73
7.1
0.158
2851
0.966
1
100
3.73-3.97
7.1
0.132
2863
0.996
1
100
3.97-4.27
7.1
0.118
2830
0.997
1
100
4.27-4.7
7
0.103
2877
1.005
1
100
4.7-5.38
6.8
0.092
2860
1.031
1
100
5.38-6.78
6.9
0.092
2879
1.114
1
100
6.78-50
7
0.102
2895
1.018
1
98.7
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
REFMAC
refinement
PDB_EXTRACT
3.11
dataextraction
HKL-2000
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
MOLREP
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.37 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.2311 / WRfactor Rwork: 0.2008 / Occupancy max: 1 / Occupancy min: 0.62 / FOM work R set: 0.8609 / SU B: 14.915 / SU ML: 0.167 / SU R Cruickshank DPI: 0.3263 / SU Rfree: 0.2304 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.326 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2285
2828
5 %
RANDOM
Rwork
0.1973
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obs
0.1988
56835
99.78 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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