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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
3J1Z
pdb_00003j1z
10.2210/pdb3j1z/pdb
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FASTA
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Binary MMCIF
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Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
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Binary MMCIF Zipped(.gz)
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Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
YiiP from Shewanella oneidensis in DOPG lipids
Specimen Preperation
Sample Aggregation State
2D ARRAY
Vitrification Instrument
GATAN CRYOPLUNGE 3
Cryogen Name
ETHANE
Sample Vitrification Details
Blot for 2-5 seconds before plunging into liquid ethane (Gatan cryoplunger)
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
?
Reported Resolution (Å)
13
Resolution Method
?
Other Details
CRYSTAL CELL PARAMETERS WERE A=57.5, B=34.0, C=100.0, ALPHA=90, BETA=90, GAMMA=85.3.
Refinement Type
Symmetry Type
HELICAL
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
?
Overall B Value
?
Fitting Procedure
?
Details
METHOD--MDFF DETAILS--An initial homology model of YiiP from S. oneidensis was built with MODELLER 9v7 using the X-ray crystal structure of YiiP from E. coli (PDB entry 3H90) as a template. This model included 9 residues at the N-terminus and 4 residues at the C-terminus that were not present in the X-ray structure. Initial configurations were obtained by manually placing the symmetry axis of the homology model onto the symmetry axis of the electron density map and aligning the protein C-terminal domains to the corresponding densities. In the first step of the MDFF fitting, harmonic potentials were applied to (a) the four-helix bundle formed by helices M1, M2, M4, and M5 (residues 12-32, 42-65, 119-142, and 147-165, respectively), (b) the M3 and M6 helices at the dimeric interface (residues 78-108 and 179-211, respectively), and (c) the C-terminal intracellular domain (residues 212-297).
Data Acquisition
Detector Type
GENERIC FILM
Electron Dose (electrons/Å
2
)
10
Imaging Experiment
Date of Experiment
2009-02-10
Temprature (Kelvin)
Microscope Model
FEI TECNAI F20
Minimum Defocus (nm)
1600
Maximum Defocus (nm)
3000
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
2.1
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
?
Nominal Magnification
50000
Calibrated Magnification
51190
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
RECONSTRUCTION
EMIP
?
RECONSTRUCTION
SPARX
?
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
.
Corrected throughout the reconstruction cycle
