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

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Basic information

Entry
Database: PDB / ID: 4acl
Title3D Structure of DotU from Francisella novicida
ComponentsTSSL
KeywordsPROTEIN TRANSPORT / T6SS / MICROBIAL SURFACE STRUCTURES / MEMBRANE PROTEIN / VIRULENCE FACTOR
Function / homology
Function and homology information


Type 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
Similarity search - Domain/homology
: / Type IV / VI secretion system DotU domain-containing protein
Similarity search - Component
Biological speciesFRANCISELLA NOVICIDA (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.49 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 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Other
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Sep 13, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.source
Revision 1.4May 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_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)51,12817
Polymers48,6172
Non-polymers2,51115
Water72140
1
A: TSSL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,63710
Polymers24,3081
Non-polymers1,3299
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TSSL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4907
Polymers24,3081
Non-polymers1,1826
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.309, 85.314, 66.989
Angle α, β, γ (deg.)90.00, 102.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TSSL


Mass: 24308.490 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Au
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.25 Å3/Da / Density % sol: 45.5 % / Description: NONE
Crystal growpH: 8 / Details: 0.1 M TRIS, PH 8.8, 20% PEG 3350.

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Apr 26, 2010 / Details: OSMIC BLUE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.49→65.99 Å / Num. obs: 15228 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 13.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.1 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
d*TREKdata reduction
d*TREKdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.49→65.43 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.891 / SU B: 10.962 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 0.473 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27867 754 5 %RANDOM
Rwork0.2181 ---
obs0.22117 14199 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.297 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20 Å20.17 Å2
2--2.55 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.49→65.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 0 21 40 2626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222635
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9633564
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8945310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.81624.851134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.13315471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.42159
X-RAY DIFFRACTIONr_chiral_restr0.1270.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021977
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_it0.9011.51549
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68222503
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.18331086
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5094.51060
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: 2.489→2.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 66 -
Rwork0.239 945 -
obs--91.08 %

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