- PDB-3fu1: Crystal structure of the major pseudopilin from the type 2 secret... -
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Basic information
Entry
Database: PDB / ID: 3fu1
Title
Crystal structure of the major pseudopilin from the type 2 secretion system of Vibrio cholerae
Components
General secretion pathway protein G
Keywords
PROTEIN TRANSPORT / GENERAL SECRETORY PATHWAY / MAJOR PILIN / COMPLEX / Methylation / Transport
Function / homology
Function and homology information
protein secretion by the type II secretion system / type II protein secretion system complex / plasma membrane Similarity search - Function
Type II secretion system protein GspG / Type II secretion system protein GspG, C-terminal / Type II secretion system (T2SS), protein G / Glycoprotein, Type 4 Pilin / Bacterial general secretion pathway protein G-type pilin / Glycoprotein, Type 4 Pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like ...Type II secretion system protein GspG / Type II secretion system protein GspG, C-terminal / Type II secretion system (T2SS), protein G / Glycoprotein, Type 4 Pilin / Bacterial general secretion pathway protein G-type pilin / Glycoprotein, Type 4 Pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
THIS CRYSTAL FORM CONTAINS A DIMER, THAT IS NOT RELATED TO THE BIOLOGICAL FORM. BIOLOGICAL UNIT IS A FIBER, IT IS UNKNOWN AT THE MOMENT HOW INDIVIDUAL SUBUNITS ARE ASSEMBLED IN VIVO.
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Components
#1: Protein
GeneralsecretionpathwayproteinG / Cholera toxin secretion protein epsG
Mass: 12579.704 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 35-146 Source method: isolated from a genetically manipulated source Details: RESIDUES 26-137 / Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: 569B / Gene: epsG, VC_2730 / Plasmid: pCDF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P45773
Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 22.5% PEG 3350, 0.1M NA ACETATE, 0.04M ZN ACETATE, pH 5.0, vapor diffusion, sitting drop, temperature 298K
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
1,2
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
SSRL
BL9-2
1
0.97946
SYNCHROTRON
SSRL
BL9-2
2
1.28344
Detector
Type
ID
Detector
Date
MARMOSAIC 325 mm CCD
1
CCD
Nov 15, 2007
MARMOSAIC 325 mm CCD
2
CCD
Nov 15, 2007
Radiation
ID
Monochromator
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
DOUBLECRYSTALSI(111)
SINGLEWAVELENGTH
M
x-ray
1
2
DOUBLECRYSTALSI(111)
SINGLEWAVELENGTH
M
x-ray
2
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.97946
1
2
1.28344
1
Reflection
Redundancy: 6.7 % / Av σ(I) over netI: 24.02 / Number: 113449 / Rmerge(I) obs: 0.087 / Χ2: 1.43 / D res high: 1.9 Å / D res low: 29 Å / Num. obs: 17045 / % possible obs: 97.1
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
4.09
29
99.9
1
0.04
1.896
6.8
3.25
4.09
100
1
0.048
1.673
7.2
2.84
3.25
100
1
0.087
1.593
7.3
2.58
2.84
100
1
0.132
1.331
7.3
2.39
2.58
100
1
0.174
1.271
7.3
2.25
2.39
100
1
0.229
1.281
7.3
2.14
2.25
99.7
1
0.291
1.289
7
2.05
2.14
98.1
1
0.371
1.245
6.3
1.97
2.05
93.5
1
0.478
1.232
5.3
1.9
1.97
78.8
1
0.512
1.226
4.1
Reflection
Resolution: 1.9→29 Å / Num. obs: 17045 / % possible obs: 97.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.428 / Net I/σ(I): 24.016
Reflection shell
Resolution: 1.9→1.97 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1373 / Χ2: 1.226 / % possible all: 78.8
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Phasing
Phasing
Method: molecular replacement
Phasing MR
Model details: Phaser MODE: MR_AUTO
Highest resolution
Lowest resolution
Rotation
2.5 Å
29.04 Å
Translation
2.5 Å
29.04 Å
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
PHASER
phasing
REFMAC
refinement
PDB_EXTRACT
3.006
dataextraction
Blu-Ice
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.28 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.875 / SU B: 6.78 / SU ML: 0.101 / SU R Cruickshank DPI: 0.172 / SU Rfree: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.223
830
4.9 %
RANDOM
Rwork
0.178
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obs
0.18
16995
96.88 %
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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: BABINET MODEL WITH MASK
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