- PDB-5ee1: Crystal structure of OsYchF1 at pH 7.85 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5ee1
Title
Crystal structure of OsYchF1 at pH 7.85
Components
Obg-like ATPase 1
Keywords
HYDROLASE / osychf1 / GTP-BINDING PROTEIN / ATP / AMP-PNP / YchF-type / P-Loop NTPase
Function / homology
Function and homology information
negative regulation of response to salt stress / negative regulation of defense response to bacterium / ribosomal large subunit binding / response to salt stress / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding ...negative regulation of response to salt stress / negative regulation of defense response to bacterium / ribosomal large subunit binding / response to salt stress / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2.55→50 Å / Num. all: 16008 / Num. obs: 15955 / % possible obs: 99.7 % / Redundancy: 5.4 % / Net I/σ(I): 17.2
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0103
refinement
MAR345dtb
datareduction
HKL-2000
datascaling
PHASER
phasing
Refinement
Resolution: 2.55→50 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.89 / SU B: 10.54 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.531 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26285
754
4.8 %
RANDOM
Rwork
0.22948
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obs
0.23116
14816
96.15 %
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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