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- PDB-2ym0: Truncated SipD from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 2ym0
TitleTruncated SipD from Salmonella typhimurium
ComponentsCELL INVASION PROTEIN SIPD
KeywordsCELL INVASION / TYPE 3 SECRETION / T3SS / NEEDLE TIP PROTEIN / HOST PATHOGEN INTERACTION / BACTERIAL PATHOGENESIS / TIP COMPLEX
Function / homologyIpaD-like / IpaD-like / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / Up-down Bundle / extracellular region / Mainly Alpha / Cell invasion protein SipD
Function and homology information
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLunelli, M. / Kolbe, M.
CitationJournal: PLoS Pathog. / Year: 2011
Title: Crystal structure of PrgI-SipD: insight into a secretion competent state of the type three secretion system needle tip and its interaction with host ligands.
Authors: Lunelli, M. / Hurwitz, R. / Lambers, J. / Kolbe, M.
History
DepositionJun 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Experimental preparation
Category: atom_site / citation / exptl_crystal_grow
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: CELL INVASION PROTEIN SIPD
B: CELL INVASION PROTEIN SIPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0913
Polymers50,9992
Non-polymers921
Water37821
1
A: CELL INVASION PROTEIN SIPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5922
Polymers25,5001
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELL INVASION PROTEIN SIPD


Theoretical massNumber of molelcules
Total (without water)25,5001
Polymers25,5001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.801, 94.372, 117.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.975, -0.2222, -0.002823), (-0.2222, 0.9749, 0.009006), (0.000751, 0.009408, -1)
Vector: 28.16, -2.832, -55.25)

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Components

#1: Protein CELL INVASION PROTEIN SIPD / SALMONELLA INVASION PROTEIN D


Mass: 25499.508 Da / Num. of mol.: 2 / Fragment: RESIDUES 132-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Strain: SL1344 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56026
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.04 Å3/Da / Density % sol: 59.6 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PROTEIN WAS MIXED WITH EQUAL VOLUME OF SOLUTION 0.1 M MES PH 6.5 AND 12% (W/V) PEG 20000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2009 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 12938 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 63.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.77
Reflection shellResolution: 3→3.15 Å / Redundancy: 5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.42 / % possible all: 96.4

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Processing

Software
NameVersionClassification
CNS1.2.1refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.1.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J0N

2j0n


Resolution: 3→37.21 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2346361.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.224 647 5 %RANDOM
Rwork0.198 ---
obs0.198 12938 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.41 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 64.4 Å2
Baniso -1Baniso -2Baniso -3
1-8.66 Å20 Å20 Å2
2--3.84 Å20 Å2
3----12.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3→37.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3065 0 6 21 3092
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.152
X-RAY DIFFRACTIONc_mcangle_it3.743
X-RAY DIFFRACTIONc_scbond_it5.584.5
X-RAY DIFFRACTIONc_scangle_it7.886
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 105 5.1 %
Rwork0.332 1968 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GOL_FULL.PARGOL_FULL.TOP

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