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- PDB-5nbg: Structure of the cytoplasmic domain I of OutF in the D. dadantii ... -

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Basic information

Entry
Database: PDB / ID: 5nbg
TitleStructure of the cytoplasmic domain I of OutF in the D. dadantii type II secretion system
ComponentsGeneral secretion pathway protein F
KeywordsMEMBRANE PROTEIN / inner membrane protein
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / protein processing / metal ion binding / plasma membrane
Similarity search - Function
Type II secretion system protein GspF / Type II secretion system (T2SS), domain F / T2SS_GspF/T4SS_PilC conserved site / Bacterial type II secretion system protein F signature. / GspF/PilC family / Type II secretion system protein GspF domain / Type II secretion system GspF domain superfamily / Type II secretion system (T2SS), protein F / Receptor-associated Protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
General secretion pathway protein F
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZhang, H. / Gu, S.
CitationJournal: To Be Published
Title: Structure of the first cytoplasmic domain of OutF and assembly of the inner-membrane platform proteins of the D. dadantii type II secretion system
Authors: Zhang, H. / Gu, S.
History
DepositionMar 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,3352
Polymers23,3352
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, the size of the molecular is 26kDa which is double times of the monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-3 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.175, 116.175, 47.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein General secretion pathway protein F


Mass: 11667.410 Da / Num. of mol.: 2 / Fragment: UNP residues 65-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (strain 3937) (bacteria)
Strain: 3937 / Gene: outF, Dda3937_02417 / Production host: Escherichia coli (E. coli) / References: UniProt: E0SM39
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.5 Å3/Da / Density % sol: 64.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100mM sodium cacodyl ate pH 6.5, 200mM Li2SO4 and 30% PEG-400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 2.15→41.44 Å / Num. obs: 18300 / % possible obs: 99.15 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.037 / Net I/σ(I): 1.35
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.024 / Num. unique obs: 1764 / CC1/2: 0.668 / Rpim(I) all: 0.016 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C1Q

3c1q


Resolution: 2.15→82.15 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.98 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26495 1831 10 %RANDOM
Rwork0.20964 ---
obs0.21518 16469 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.982 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.15→82.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 0 53 1652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191615
X-RAY DIFFRACTIONr_bond_other_d0.0020.021617
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.9822178
X-RAY DIFFRACTIONr_angle_other_deg1.03533701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5345212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8824.0367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0215289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0721514
X-RAY DIFFRACTIONr_chiral_restr0.0920.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021842
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02348
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5294.792854
X-RAY DIFFRACTIONr_mcbond_other4.5114.788853
X-RAY DIFFRACTIONr_mcangle_it6.0437.1661064
X-RAY DIFFRACTIONr_mcangle_other6.0527.1731065
X-RAY DIFFRACTIONr_scbond_it5.8235.587761
X-RAY DIFFRACTIONr_scbond_other5.825.595762
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.5648.0751115
X-RAY DIFFRACTIONr_long_range_B_refined10.34238.661902
X-RAY DIFFRACTIONr_long_range_B_other10.35538.6151890
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 133 -
Rwork0.29 1195 -
obs--99.48 %

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