PDB-2y9k: Three-dimensional model of Salmonella's needle complex ...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 2y9k
Title	Three-dimensional model of Salmonella's needle complex at subnanometer resolution
Descriptor	PROTEIN INVG
Keywords	PROTEIN TRANSPORT, TYPE III SECRETION SYSTEM, OUTER MEMBRANE RING, SECRETIN FAMILY, C15 FOLD
Authors	Schraidt, O., Marlovits, T.C.
Date	Deposition: 2011-02-15, Release: 2011-03-23
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with EM 3D map: EMDB-1871, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1871 CiteFit EMDB-1874 Cite EMDB-1875 Cite PDB-2y9j Cite Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-3j1v EMDB-1871 PDB-2ypw List of similar structure data about Omokage system

Article
Citation - primary
Article	Science, Vol. 331, Issue 6021, Page 1192-5, Year 2011
Title	Three-dimensional model of Salmonella's needle complex at subnanometer resolution.
Authors	Oliver Schraidt, Thomas C Marlovits Research Institute of Molecular Pathology, Dr. Bohr Gasse 7, A-1030 Vienna, Austria.
Keywords	Bacterial Proteins (chemistry), Bacterial Secretion Systems, Cryoelectron Microscopy, Crystallography, X-Ray, Image Processing, Computer-Assisted, Membrane Proteins (chemistry), Membrane Transport Proteins (chemistry), Models, Molecular, Mutation, PrgH protein, Salmonella typhimurium, PrgK protein, Salmonella typhimurium, Protein Conformation, Protein Structure, Tertiary, Salmonella typhimurium (chemistry), invG protein, Salmonella typhimurium
Links	DOI: 10.1126/science.1199358, PubMed: 21385715

Components
ID 1 : PROTEIN INVG
Image
Description	PROTEIN INVG
Type	polymer
Fragment	N-TERMINAL DOMAIN, RESIDUES 34-170
Formula weight	15617.036 Da
Number of molecules	15
Source	Method: Isolated from a natural source NCBI taxonomy: ID:90371 Organism scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
Links	UniProt: P35672, Sequence view

Electron Microscopy
Imaging
Microscope	model: OTHER
Details	ACUAL MAGNIFICATION AT CCD 112968, CAMERA PIXEL SIZE 15UM, 1.33 ANGSTROM PER PIXEL, DATA COLLECTED SEMI- AUTOMATICALLY USING POINT-2-POINT (DEVELOPED IN-HOUSE)
Electron gun
Electron source	FIELD EMISSION GUN
Accelerating voltage	300 kV
Lens
Mode	BRIGHT FIELD
Magnification	nominal: 93000 X
Cs	nominal: 2 mm
Nominal defocus	max: 2500 nm, min: 1000 nm
Specimen holder
Tilt angle	min: 0 degrees
Detector
Type	CCD GATAN 4KX4K

Processing
2D projection selection
Software name	IMAGIC, CHIMERA
3D reconstruction
Actual pixel size	1.33 A/pix
CTF correction method	EACH CCD FRAME
Details	RESOLUTION 8.3 ANGSTROM (0.5 FSC), 6.7 ANGSTROM (HALF BIT) SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1871. (DEPOSITION ID: 7820).
Method	PROJECTION MATCHING
Resolution	8.3 A
3D fitting
Method	RIGID BODY FITTING
Refinement Space	REAL
Target criteria	CORRELATION
3D fitting list
PDB entry ID	3GR5 PDB-3gr5
Refine
Ls d res high	8.30 A
ID	1
Refine hist
D res high	8.30
Total atoms	16485
Protein atoms	16485