Home
About
Browse
Covid-19
Organism Classification
Alphafold Collection
Virus Classification
Indian Data
Contact
Search Type
PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
1X1L
pdb_00001x1l
10.2210/pdb1x1l/pdb
Download file
FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
THERMUS THERMOPHILUS 30S ribosomal subunit complexed with Era
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
?
Cryogen Name
?
Sample Vitrification Details
Rapid-freezing in liquid ethane
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
?
Reported Resolution (Å)
13.5
Resolution Method
?
Other Details
projection matching using spider package. The coordinates for only the alpha carbons in protein and phosphoruses in rRNA are present in the structure. The number of missing atoms was so much that remark 470 for the missing atoms list were removed.
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
X-ray coordinates of the 30S ribosomal subunit and ERA were fitted into the 13.5 angstroms resolution CRYO-EM map of the T. Thermophilus 30S subunit-ERA complex. the atomic structure of ERA was fitted as 3 rigid bodies, N-terminal domain, C-terminal domain and C-terminal helix within the C-terminal domain. The resultant ERA structure was then energy minimized. The X-ray coordinates of T. Thermophilus 30S subunit was fitted as 4 rigid bodies, head, body, platform and 16S rRNA 3' minor domains. Only the coordinates of the 16S rRNA 3' minor domain and ERA are included HERE. The KH domain of ERA makes direct contact with the 3' terminus of the 16S rRNA.
Overall B Value
?
Fitting Procedure
?
Details
METHOD--cross-correlation based manual fitting in O REFINEMENT PROTOCOL--MULTIPLE RIGID BODY
Data Acquisition
Detector Type
KODAK SO-163 FILM
Electron Dose (electrons/Å
2
)
20
Imaging Experiment
Date of Experiment
2003-03-25
Temprature (Kelvin)
Microscope Model
FEI TECNAI F20
Minimum Defocus (nm)
1180
Maximum Defocus (nm)
3940
Minimum Tilt Angle (degrees)
0
Maximum Tilt Angle (degrees)
0
Nominal CS
2.0
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
?
Nominal Magnification
50000
Calibrated Magnification
49696
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
MODEL FITTING
O
?
RECONSTRUCTION
SPIDER
?
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
.
CTF correction of 3D-maps by wiener filtration
