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- PDB-2i4s: PDZ domain of EpsC from Vibrio cholerae, residues 204-305 -

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Basic information

Entry
Database: PDB / ID: 2i4s
TitlePDZ domain of EpsC from Vibrio cholerae, residues 204-305
ComponentsGeneral secretion pathway protein C
KeywordsPROTEIN 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
Type II secretion system protein C
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsKorotkov, K.V. / Krumm, B. / Bagdasarian, M. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural and Functional Studies of EpsC, a Crucial Component of the Type 2 Secretion System from Vibrio cholerae.
Authors: Korotkov, K.V. / Krumm, B. / Bagdasarian, M. / Hol, W.G.
History
DepositionAug 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General secretion pathway protein C
B: General secretion pathway protein C


Theoretical massNumber of molelcules
Total (without water)24,3152
Polymers24,3152
Non-polymers00
Water3,891216
1
A: General secretion pathway protein C


Theoretical massNumber of molelcules
Total (without water)12,1581
Polymers12,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: General secretion pathway protein C


Theoretical massNumber of molelcules
Total (without water)12,1581
Polymers12,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.244, 25.499, 87.654
Angle α, β, γ (deg.)90.000, 125.380, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein General secretion pathway protein C / Cholera toxin secretion protein epsC


Mass: 12157.721 Da / Num. of mol.: 2 / Fragment: PDZ domain, residues 204-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: epsC / Plasmid: pProEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: P45777
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 10
Details: 2.4M ammonium sulfate, 0.2M Li sulfate, 0.1M CAPS pH 10.0, vapor diffusion, temperature 294K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979124 Å
DetectorDate: Aug 10, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.979124 Å / Relative weight: 1
ReflectionRedundancy: 3.3 % / Av σ(I) over netI: 7 / Number: 50256 / Rmerge(I) obs: 0.093 / Χ2: 1.05 / D res high: 1.94 Å / D res low: 50 Å / Num. obs: 15285 / % possible obs: 97.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.185097.810.071.4683
3.324.1899.310.0611.0813.3
2.93.3299.910.0841.2123.4
2.632.999.710.1111.2123.5
2.442.6399.610.1251.1823.4
2.32.4498.810.1381.0343.4
2.182.398.510.1550.9393.3
2.092.1896.610.1840.8333.3
2.012.099710.2140.7683.3
1.942.0189.410.2780.6792.9
ReflectionResolution: 1.94→50 Å / Num. obs: 15285 / % possible obs: 97.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.093 / Χ2: 1.051 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.94-2.012.90.27813700.67989.4
2.01-2.093.30.21415050.76897
2.09-2.183.30.18414810.83396.6
2.18-2.33.30.15515420.93998.5
2.3-2.443.40.13815111.03498.8
2.44-2.633.40.12515571.18299.6
2.63-2.93.50.11115481.21299.7
2.9-3.323.40.08415701.21299.9
3.32-4.183.30.06115711.08199.3
4.18-5030.0716301.46897.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.92→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / SU B: 3.669 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 759 5 %RANDOM
Rwork0.176 ---
all0.179 15282 --
obs0.179 15282 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.569 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.34 Å2
2---0.07 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.92→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1660 0 0 216 1876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221682
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9722270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4775208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60625.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47915306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7661512
X-RAY DIFFRACTIONr_chiral_restr0.1010.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021296
X-RAY DIFFRACTIONr_nbd_refined0.2540.3776
X-RAY DIFFRACTIONr_nbtor_refined0.3110.51168
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.5280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.362
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.538
X-RAY DIFFRACTIONr_mcbond_it2.8841071
X-RAY DIFFRACTIONr_mcangle_it3.861686
X-RAY DIFFRACTIONr_scbond_it5.2346667
X-RAY DIFFRACTIONr_scangle_it6.3128584
LS refinement shellResolution: 1.924→1.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 42 -
Rwork0.204 864 -
obs-906 77.24 %

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