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- PDB-2fm8: Crystal Structure of the Salmonella Secretion Chaperone InvB in C... -

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Basic information

Entry
Database: PDB / ID: 2fm8
TitleCrystal Structure of the Salmonella Secretion Chaperone InvB in Complex with SipA
Components
  • Cell invasion protein sipA
  • Surface presentation of antigens protein spaK
KeywordsCHAPERONE/CELL INVASION / type III secretion / chaperone / translocation / protein folding / virulence / Salmonella / bacterial / CHAPERONE-CELL INVASION COMPLEX
Function / homology
Function and homology information


actin binding / extracellular region
Similarity search - Function
SipA N-terminal domain-like / SipA N-terminal domain-like / Surface presentation of antigens protein SpaK / Invasion protein B family / Salmonella invasion protein A, C-terminal actin-binding domain superfamily / : / Salmonella Invasion protein A, C-terminal actin binding domain / Salmonella invasion protein A, N-terminal / Salmonella invasion protein A, chaperone-binding / SipA N-terminal domain ...SipA N-terminal domain-like / SipA N-terminal domain-like / Surface presentation of antigens protein SpaK / Invasion protein B family / Salmonella invasion protein A, C-terminal actin-binding domain superfamily / : / Salmonella Invasion protein A, C-terminal actin binding domain / Salmonella invasion protein A, N-terminal / Salmonella invasion protein A, chaperone-binding / SipA N-terminal domain / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Surface presentation of antigens protein SpaK / Cell invasion protein SipA / Cell invasion protein SipA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsLilic, M. / Vujanac, M. / Stebbins, C.E.
CitationJournal: Mol.Cell / Year: 2006
Title: A common structural motif in the binding of virulence factors to bacterial secretion chaperones.
Authors: Lilic, M. / Vujanac, M. / Stebbins, C.E.
History
DepositionJan 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Surface presentation of antigens protein spaK
B: Surface presentation of antigens protein spaK
C: Cell invasion protein sipA


Theoretical massNumber of molelcules
Total (without water)55,9313
Polymers55,9313
Non-polymers00
Water11,025612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-34 kcal/mol
Surface area23500 Å2
MethodPISA
2
A: Surface presentation of antigens protein spaK
B: Surface presentation of antigens protein spaK
C: Cell invasion protein sipA

A: Surface presentation of antigens protein spaK
B: Surface presentation of antigens protein spaK
C: Cell invasion protein sipA


Theoretical massNumber of molelcules
Total (without water)111,8626
Polymers111,8626
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area15320 Å2
ΔGint-95 kcal/mol
Surface area43350 Å2
MethodPISA
3
A: Surface presentation of antigens protein spaK
B: Surface presentation of antigens protein spaK
C: Cell invasion protein sipA

A: Surface presentation of antigens protein spaK
B: Surface presentation of antigens protein spaK
C: Cell invasion protein sipA


Theoretical massNumber of molelcules
Total (without water)111,8626
Polymers111,8626
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area15060 Å2
ΔGint-81 kcal/mol
Surface area43610 Å2
MethodPISA
4
B: Surface presentation of antigens protein spaK

B: Surface presentation of antigens protein spaK

A: Surface presentation of antigens protein spaK
C: Cell invasion protein sipA

A: Surface presentation of antigens protein spaK
C: Cell invasion protein sipA


Theoretical massNumber of molelcules
Total (without water)111,8626
Polymers111,8626
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation8_665x-y+1,-y+1,-z1
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area10180 Å2
ΔGint-67 kcal/mol
Surface area48490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.505, 146.505, 156.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Surface presentation of antigens protein spaK / Invasion protein invB


Mass: 14931.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: spaK, invB / Plasmid: pGEX-4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A1N0
#2: Protein Cell invasion protein sipA / Effector protein sipA


Mass: 26068.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: sipA, sspA / Plasmid: pGEX-4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q56027, UniProt: P0CL52*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 4.34 Å3/Da / Density % sol: 71.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 27mg/ml protein with an equilibration buffer consisting of 3.8M Na-formate, 0.9M Na-cacodylate pH 5.2 and 0.09M guanidine-hydrochloride as an additive, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. all: 66495 / Num. obs: 66495 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.072 / Χ2: 1.051
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0 / Num. unique all: 6487 / Χ2: 0.898 / % possible all: 98.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→99 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.943 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2514 5.1 %RANDOM
Rwork0.198 ---
all0.2 49515 --
obs0.19999 49515 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.011 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.33 Å20 Å2
2---0.65 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.2→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3693 0 0 612 4305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223749
X-RAY DIFFRACTIONr_bond_other_d0.0020.023484
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9775064
X-RAY DIFFRACTIONr_angle_other_deg0.82138116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49525.472159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62815678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.961514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024123
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02694
X-RAY DIFFRACTIONr_nbd_refined0.220.2866
X-RAY DIFFRACTIONr_nbd_other0.180.23352
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21830
X-RAY DIFFRACTIONr_nbtor_other0.0860.22117
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.2454
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0930.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.230
X-RAY DIFFRACTIONr_mcbond_it1.261.53086
X-RAY DIFFRACTIONr_mcbond_other0.1961.5979
X-RAY DIFFRACTIONr_mcangle_it1.4623798
X-RAY DIFFRACTIONr_scbond_it2.59331560
X-RAY DIFFRACTIONr_scangle_it3.6894.51266
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 184 -
Rwork0.228 3479 -
obs-3663 98.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3651-0.3121.11830.7501-0.15251.27670.0765-0.2357-0.09170.07720.0370.00690.0902-0.0711-0.1135-0.0767-0.0081-0.07460.06860.033-0.05032.91248.0919.571
21.94960.58330.00621.3697-0.71881.05420.133-0.0859-0.2758-0.0248-0.095-0.04350.1315-0.008-0.0381-0.0789-0.0449-0.07390.02060.02730.0143-17.76238.727.286
35.48180.8161-1.88211.44571.61826.76160.0102-0.57140.02680.16370.0228-0.03870.27790.235-0.033-0.0599-0.0061-0.089-0.0190.0548-0.11698.2351.63825.684
41.0524-0.3540.21780.8672-0.16380.31220.0342-0.0240.09090.02220.01-0.0433-0.01280.0476-0.0442-0.0794-0.0275-0.0020.02040.003-0.0264-25.37375.099-1.584
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 1341 - 134
22BB1 - 1351 - 135
33CC23 - 441 - 22
44CC52 - 26230 - 240

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