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- PDB-4ack: 3D Structure of DotU from Francisella novicida -

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Basic information

Entry
Database: PDB / ID: 4ack
Title3D Structure of DotU from Francisella novicida
ComponentsTSSL
KeywordsPROTEIN TRANSPORT / T6SS / MICROBIAL SURFACE STRUCTURES / VIRULENCE FACTOR
Function / homologyType IV / VI secretion system, DotU / Type IV / VI secretion system, DotU / Type IV / VI secretion system, DotU superfamily / Type VI secretion system protein DotU / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / BROMIDE ION / Type IV / VI secretion system DotU domain-containing protein
Function and homology information
Biological speciesFRANCISELLA NOVICIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.15 Å
AuthorsRobb, C.S. / Nano, F.E. / Boraston, A.B.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The Structure of the Conserved Type Six Secretion Protein Tssl (Dotu) from Francisella Novicida
Authors: Robb, C.S. / Nano, F.E. / Boraston, A.B.
History
DepositionDec 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Other
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TSSL
B: TSSL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,96612
Polymers44,2742
Non-polymers69210
Water2,504139
1
A: TSSL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3594
Polymers22,1371
Non-polymers2223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TSSL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6078
Polymers22,1371
Non-polymers4707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.660, 85.840, 67.710
Angle α, β, γ (deg.)90.00, 102.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TSSL


Mass: 22137.117 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 1-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FRANCISELLA NOVICIDA (bacteria) / Strain: U112 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: A0Q7H7
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.85 % / Description: NONE
Crystal growpH: 8 / Details: 0.115 M KBR, 0.1 M TRIS, PH 8.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.92
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.15→65.99 Å / Num. obs: 24116 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.9
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALEPACKdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.15→65.99 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.774 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A23-25 B24 B113-114 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.25118 1227 5.1 %RANDOM
Rwork0.19391 ---
obs0.19691 22858 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20 Å2-0.55 Å2
2--2.42 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.15→65.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 28 139 2743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222679
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.9643606
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.06424.892139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.21115498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.775159
X-RAY DIFFRACTIONr_chiral_restr0.1250.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021993
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3171.51539
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.40122502
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.36331140
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2424.51103
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.345 90 -
Rwork0.239 1726 -
obs--99.89 %

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