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- PDB-3rx9: 3D structure of SciN from an Escherichia coli Patotype -

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Basic information

Entry
Database: PDB / ID: 3rx9
Title3D structure of SciN from an Escherichia coli Patotype
ComponentsPutative uncharacterized protein
KeywordsLIPID BINDING PROTEIN / transthyretin (1sn5) fold / lipoprotein / T6SS assembly / SciS
Function / homologyType VI secretion system, lipoprotein SciN / Type VI secretion system, lipoprotein SciN / Type VI secretion protein SciN-like superfamily / Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta / Type VI secretion system lipoprotein TssJ
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsFelisberto-Rodrigues, C. / Durand, E. / Aschtgen, M.-S. / Blangy, S. / Ortiz-Lombardia, M. / Douzy, B. / Cambillau, C. / Cascales, E.
CitationJournal: Plos Pathog. / Year: 2011
Title: Towards a Structural Comprehension of Bacterial Type VI Secretion Systems: Characterization of the TssJ-TssM Complex of an Escherichia coli Pathovar.
Authors: Felisberto-Rodrigues, C. / Durand, E. / Aschtgen, M.S. / Blangy, S. / Ortiz-Lombardia, M. / Douzi, B. / Cambillau, C. / Cascales, E.
History
DepositionMay 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0712
Polymers16,9751
Non-polymers961
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.070, 78.070, 46.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Putative uncharacterized protein


Mass: 16975.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 55989 / EAEC / Gene: EC55989_3320, NC_011748.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B7LFS8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: mixing 300 nL protein at 8mg/mL with 100 nL 2.2 M AmSO4, 0.2 M Na+-thiocyanate pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2011
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.35→45 Å / Num. all: 35308 / Num. obs: 35308 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.1
Reflection shellResolution: 1.35→1.39 Å / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.8 / % possible all: 79.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CsI SAD crystal structure

Resolution: 1.35→40 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.275 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.15982 1773 5 %RANDOM
Rwork0.13683 ---
obs0.13798 33535 96.63 %-
all-33535 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å2-0 Å2
2--0.42 Å2-0 Å2
3----0.62 Å2
Refine analyzeLuzzati coordinate error free: 0.045 Å
Refinement stepCycle: LAST / Resolution: 1.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 5 200 1205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021204
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9861675
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7235173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50624.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10715217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0591511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021955
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr2.431204
X-RAY DIFFRACTIONr_sphericity_free24.427545
X-RAY DIFFRACTIONr_sphericity_bonded13.56851319
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 94 -
Rwork0.202 1938 -
obs--78.82 %
Refinement TLS params.Method: refined / Origin x: -17.3791 Å / Origin y: 36.3314 Å / Origin z: -4.3242 Å
111213212223313233
T0.009 Å20.0001 Å2-0.0007 Å2-0.0086 Å2-0 Å2--0.0012 Å2
L0.0064 °20.0026 °2-0.0078 °2-0.0284 °2-0.0088 °2--0.0171 °2
S0.0012 Å °-0.0007 Å °0.0015 Å °0.0016 Å °-0.0005 Å °0.0017 Å °0.0021 Å °-0.0001 Å °-0.0007 Å °

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