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- PDB-2i6v: PDZ domain of EpsC from Vibrio cholerae, residues 219-305 -

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Basic information

Entry
Database: PDB / ID: 2i6v
TitlePDZ domain of EpsC from Vibrio cholerae, residues 219-305
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 / SAD / Resolution: 1.63 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 29, 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
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: General secretion pathway protein C


Theoretical massNumber of molelcules
Total (without water)9,9351
Polymers9,9351
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.182, 44.884, 51.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 9935.156 Da / Num. of mol.: 1 / Fragment: PDZ domain, residues 219-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: epsC / Plasmid: AVA0421 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45777
#2: Water ChemComp-HOH / water


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

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

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 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
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2030B / Detector: IMAGE PLATE / Date: May 3, 2005 / Details: Osmic optics
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 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) obsRsym valueChi squaredRedundancy
4.5920.73950.0520.0522.676
3.244.5998.90.0460.0462.5226.6
2.653.2497.90.0490.0492.57
2.292.6597.70.0660.0662.4147.1
2.052.2997.70.0840.0842.4257.1
1.872.0596.60.1140.1142.3777.2
1.731.8791.80.1630.1632.4957.1
1.621.7359.60.2620.2622.6046.6
1.531.62370.3490.3492.7876.3
1.451.5324.10.5260.5263.4845
ReflectionResolution: 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 shellResolution: 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
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
DIPV. 2000data collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.203 506 4.8 %RANDOM
Rwork0.17 ---
all0.171 ---
obs-10520 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.292 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.63→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms707 0 0 117 824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022719
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.97973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70825.64139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3815129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.396154
X-RAY DIFFRACTIONr_chiral_restr0.0790.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02558
X-RAY DIFFRACTIONr_nbd_refined0.2220.3267
X-RAY DIFFRACTIONr_nbtor_refined0.3210.5496
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.531
X-RAY DIFFRACTIONr_mcbond_it1.8094450
X-RAY DIFFRACTIONr_mcangle_it2.6016711
X-RAY DIFFRACTIONr_scbond_it2.7816297
X-RAY DIFFRACTIONr_scangle_it4.3028262
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 52 -
Rwork0.234 693 -
obs-745 97.51 %

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