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- PDB-3eaa: Structure of a type six secretion system protein -

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Basic information

Entry
Database: PDB / ID: 3eaa
TitleStructure of a type six secretion system protein
ComponentsEvpC
KeywordsUNKNOWN FUNCTION / EvpC / T6SS
Function / homologyHcp1-like / : / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Pnp Oxidase; Chain A / Roll / Mainly Beta / EvpC
Function and homology information
Biological speciesEdwardsiella tarda (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.794 Å
AuthorsJobichen, C. / Sivaraman, J.
CitationJournal: Plos One / Year: 2010
Title: Structural basis for the secretion of EvpC: a key type VI secretion system protein from Edwardsiella tarda
Authors: Jobichen, C. / Chakraborty, S. / Li, M. / Zheng, J. / Joseph, L. / Mok, Y.K. / Leung, K.Y. / Sivaraman, J.
History
DepositionAug 25, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EvpC
B: EvpC


Theoretical massNumber of molelcules
Total (without water)36,2472
Polymers36,2472
Non-polymers00
Water68538
1
A: EvpC
x 6


Theoretical massNumber of molelcules
Total (without water)108,7426
Polymers108,7426
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area17300 Å2
ΔGint-135 kcal/mol
Surface area38750 Å2
MethodPISA
2
B: EvpC
x 6


Theoretical massNumber of molelcules
Total (without water)108,7426
Polymers108,7426
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area17300 Å2
ΔGint-134 kcal/mol
Surface area38900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.459, 85.459, 93.066
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 2:163 )
21chain B and (resseq 2:163 )

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 2 - 163 / Label seq-ID: 2 - 163

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein EvpC


Mass: 18123.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Edwardsiella tarda (bacteria) / Plasmid: pETM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6EE19
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Ammonium sulphate, 0.1M BIS-TRIS(pH 6.5), 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 30, 2007
RadiationMonochromator: CN1707 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.794→50 Å / Num. all: 9595 / Num. obs: 9073 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 33.95 Å2 / Rsym value: 0.163 / Net I/σ(I): 7.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementStarting model: PDB code 1Y12

1y12


Resolution: 2.794→28.963 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 2.2 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.284 434 4.78 %Random
Rwork0.238 8639 --
obs0.241 9073 93.91 %-
all-9595 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.433 Å2 / ksol: 0.226 e/Å3
Displacement parametersBiso max: 140.79 Å2 / Biso mean: 27.644 Å2 / Biso min: 6.65 Å2
Baniso -1Baniso -2Baniso -3
1--4.371 Å20 Å20 Å2
2---4.371 Å2-0 Å2
3---8.741 Å2
Refinement stepCycle: LAST / Resolution: 2.794→28.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 0 38 2380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072400
X-RAY DIFFRACTIONf_angle_d1.0323252
X-RAY DIFFRACTIONf_chiral_restr0.063348
X-RAY DIFFRACTIONf_plane_restr0.003422
X-RAY DIFFRACTIONf_dihedral_angle_d18.624800
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1174X-RAY DIFFRACTIONPOSITIONAL
12B1174X-RAY DIFFRACTIONPOSITIONAL0.015
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.794-3.1980.3261270.2522781290891
3.198-4.0270.2881570.2472775293291
4.027-28.9650.2481500.213083323399

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