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- PDB-3zqe: PrgI-SipD from Salmonella typhimurium in complex with deoxycholate -

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Basic information

Entry
Database: PDB / ID: 3zqe
TitlePrgI-SipD from Salmonella typhimurium in complex with deoxycholate
ComponentsPROTEIN PRGI, CELL INVASION PROTEIN SIPD
KeywordsCELL INVASION / CELL INVASION COMPLEX / TYPE III SECRETION / T3SS / TIP COMPLEX / HOST PATHOGEN INTERACTION / BACTERIAL PATHOGENESIS / BILE SALT
Function / homology
Function and homology information


type III protein secretion system complex / protein secretion by the type III secretion system / cell surface / extracellular region / identical protein binding
Similarity search - Function
IpaD-like / IpaD-like / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
SPI-1 type 3 secretion system needle filament protein / Cell invasion protein SipD
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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 9, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 1.2Dec 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: PROTEIN PRGI, CELL INVASION PROTEIN SIPD
B: PROTEIN PRGI, CELL INVASION PROTEIN SIPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8955
Polymers66,3182
Non-polymers5773
Water1,74797
1
A: PROTEIN PRGI, CELL INVASION PROTEIN SIPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3433
Polymers33,1591
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN PRGI, CELL INVASION PROTEIN SIPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5512
Polymers33,1591
Non-polymers3931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)171.152, 47.456, 102.627
Angle α, β, γ (deg.)90.00, 121.96, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6858, -0.6888, 0.235), (-0.6827, 0.4972, -0.5354), (0.252, -0.5276, -0.8112)
Vector: 38.67, 24.07, 17.28)

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Components

#1: Protein PROTEIN PRGI, CELL INVASION PROTEIN SIPD / SALMONELLA INVASION PROTEIN D / PRGI-SIPD FUSION PROTEIN


Mass: 33158.875 Da / Num. of mol.: 2 / Fragment: PRGI FUSED WITH SIPD RESIDUES 127-343
Source method: isolated from a genetically manipulated source
Details: GGSGG LINK INSERTED BETWEEN PRGI AND SIPD
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: P41784, UniProt: Q56026
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O4 / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID (DXC): HETSYN DXC DEOXYCHOLIC ACID
Sequence detailsRESIDUES GSH AT THE N-TERMINUS REMAINING AFTER HIS-TAG CLEAVAGE. GGSGG LINKER INSERTED BETWEEN PRGI ...RESIDUES GSH AT THE N-TERMINUS REMAINING AFTER HIS-TAG CLEAVAGE. GGSGG LINKER INSERTED BETWEEN PRGI AND SIPD127-343.

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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: 2.67 Å3/Da / Density % sol: 53.9 % / Description: NONE
Crystal growDetails: PROTEIN WAS MIXED WITH SOLUTION CONTAINING 0.026 M NAH2PO4 AND 1.26 M K2HPO4. OBTAINED CRYSTALS WERE SOAKED FOR 72 HOURS IN SAME SOLUTION CONTAINING 0.01 M DEOXYCHOLATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 4, 2010 / 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: 2.19→40 Å / Num. obs: 34906 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.02
Reflection shellResolution: 2.19→2.26 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.73 / % possible all: 84.4

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Processing

Software
NameVersionClassification
CNS1.21refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.1.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZQB

3zqb


Resolution: 2.19→36.48 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3170360.76 / 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. THE CHAINS WERE RENUMBERED TO BE CONSISTENT WITH NUMBERING OF THE BIOLOGICALLY ACTIVE MOLECULES FOR WHICH THERE ARE EXISTING PDB AND UNIPROT ENTRIES.
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1728 5 %RANDOM
Rwork0.246 ---
obs0.246 34906 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.4442 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 53.2 Å2
Baniso -1Baniso -2Baniso -3
1--9.88 Å20 Å21.03 Å2
2--0.7 Å20 Å2
3---9.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.19→36.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4006 0 40 97 4143
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_d18.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.12
X-RAY DIFFRACTIONc_mcangle_it3.263
X-RAY DIFFRACTIONc_scbond_it5.264.5
X-RAY DIFFRACTIONc_scangle_it6.886
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.19→2.33 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.497 248 4.9 %
Rwork0.467 4838 -
obs--84.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GOL_FULL.PARGOL_FULL.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5DXC.PARDXC.TOP

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