- PDB-2i6v: PDZ domain of EpsC from Vibrio cholerae, residues 219-305 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2i6v
Title
PDZ domain of EpsC from Vibrio cholerae, residues 219-305
Components
General secretion pathway protein C
Keywords
PROTEIN TRANSPORT / MEMBRANE PROTEIN / EpsC / GspC / PDZ domain / Type 2 Secretion System / General Secretion Pathway
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 GspC / Bacterial type II secretion system protein C signature. / Type II secretion system protein GspC, N-terminal / Type II secretion system protein C / PDZ domain / Pdz3 Domain / PDZ superfamily / Roll / Mainly Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal grow
Temperature: 294 K / Method: vapor diffusion / pH: 7.8 Details: 1.9M ammonium sulfate, 0.2M Li sulfate, 0.1M Tris pH 7.8, vapor diffusion, temperature 294K
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
1
Diffraction source
Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
Detector
Type: MAC Science DIP-2030B / Detector: IMAGE PLATE / Date: May 3, 2005 / Details: Osmic optics
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
SINGLEWAVELENGTH
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
1
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Redundancy: 6.8 % / Av σ(I) over netI: 7.1 / Number: 74457 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Χ2: 2.61 / D res high: 1.45 Å / D res low: 33.911 Å / Num. obs: 10912 / % possible obs: 72.8
Diffraction reflection shell
ID: 1
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
Rmerge(I) obs
Rsym value
Chi squared
Redundancy
4.59
20.73
95
0.052
0.052
2.67
6
3.24
4.59
98.9
0.046
0.046
2.522
6.6
2.65
3.24
97.9
0.049
0.049
2.5
7
2.29
2.65
97.7
0.066
0.066
2.414
7.1
2.05
2.29
97.7
0.084
0.084
2.425
7.1
1.87
2.05
96.6
0.114
0.114
2.377
7.2
1.73
1.87
91.8
0.163
0.163
2.495
7.1
1.62
1.73
59.6
0.262
0.262
2.604
6.6
1.53
1.62
37
0.349
0.349
2.787
6.3
1.45
1.53
24.1
0.526
0.526
3.484
5
Reflection
Resolution: 1.63→50 Å / Num. obs: 10558 / % possible obs: 99.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.044 / Χ2: 2.614 / Net I/σ(I): 57.6
Reflection shell
Resolution: 1.63→1.69 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 16.7 / Num. unique all: 1004 / Χ2: 3.484 / % possible all: 97.3
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
REFMAC
5.2.0019
refinement
PDB_EXTRACT
2
dataextraction
DIP
V. 2000
datacollection
HKL-2000
datascaling
SOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.63→28.99 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.732 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.203
506
4.8 %
RANDOM
Rwork
0.17
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all
0.171
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obs
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10520
99.46 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 18.292 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.17 Å2
0 Å2
0 Å2
2-
-
0.11 Å2
0 Å2
3-
-
-
0.06 Å2
Refinement step
Cycle: LAST / Resolution: 1.63→28.99 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
707
0
0
117
824
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.022
719
X-RAY DIFFRACTION
r_angle_refined_deg
1.108
1.97
973
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.63
5
88
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.708
25.641
39
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.38
15
129
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.396
15
4
X-RAY DIFFRACTION
r_chiral_restr
0.079
0.2
107
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
558
X-RAY DIFFRACTION
r_nbd_refined
0.222
0.3
267
X-RAY DIFFRACTION
r_nbtor_refined
0.321
0.5
496
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.173
0.5
149
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.123
0.3
53
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.181
0.5
31
X-RAY DIFFRACTION
r_mcbond_it
1.809
4
450
X-RAY DIFFRACTION
r_mcangle_it
2.601
6
711
X-RAY DIFFRACTION
r_scbond_it
2.781
6
297
X-RAY DIFFRACTION
r_scangle_it
4.302
8
262
LS refinement shell
Resolution: 1.63→1.672 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.345
52
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Rwork
0.234
693
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obs
-
745
97.51 %
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