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- PDB-3epu: Crystal Structure of STM2138, a novel virulence chaperone in Salm... -

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Basic information

Entry
Database: PDB / ID: 3epu
TitleCrystal Structure of STM2138, a novel virulence chaperone in Salmonella
ComponentsSTM2138 Virulence Chaperone
KeywordsCHAPERONE / Virulence Chaperone / Salmonella / TypeIII Secretion System / STM2138 / SrcA (SsrB-regulated chaperone A)
Function / homology
Function and homology information


protein secretion by the type III secretion system
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #740 / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, K. / Andres, S.N. / Hannemann, M. / Coombes, B. / Junop, M.
CitationJournal: To be Published
Title: Structural analysis and quantitative proteomic interactome of a novel virulence chaperone in Salmonella
Authors: Cooper, C. / Zhang, K. / Andres, S.N. / Hannemann, M. / Junop, M.S. / Coombes, B.
History
DepositionSep 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 13, 2013Group: Refinement description
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: STM2138 Virulence Chaperone
B: STM2138 Virulence Chaperone


Theoretical massNumber of molelcules
Total (without water)33,8142
Polymers33,8142
Non-polymers00
Water1,54986
1
A: STM2138 Virulence Chaperone
B: STM2138 Virulence Chaperone

A: STM2138 Virulence Chaperone
B: STM2138 Virulence Chaperone


Theoretical massNumber of molelcules
Total (without water)67,6284
Polymers67,6284
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8660 Å2
ΔGint-58 kcal/mol
Surface area27650 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-18 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.838, 46.832, 65.936
Angle α, β, γ (deg.)90.00, 106.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein STM2138 Virulence Chaperone


Mass: 16906.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: STM2138 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta(DE3) / References: UniProt: Q8ZNP3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Bis-Tris propane, 200 mM MgCl2, 35% PEG 3350, 3.95 mM FOS-choline-9, 5% (v/v) Jeffamine M-600, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 24, 2008 / Details: toroidal mirror
RadiationMonochromator: Si(111) channel-cut crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. all: 10664 / Num. obs: 10664 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.62 % / Biso Wilson estimate: 54.8 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.5
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.4 / % possible all: 94.6

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K3E

1k3e


Resolution: 2.5→33.4 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.931 / SU B: 16.719 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST 2 TLS GROUPS CORRESPONDS TO THE MAIN CHAIN ATOMS AND THE TLS-3,4 CORRESPONDS TO THE SIDE-CHAINS OF THE SAME RESIDUES
RfactorNum. reflection% reflectionSelection details
Rfree0.25256 538 5 %RANDOM
Rwork0.21448 ---
obs0.21635 10170 99.91 %-
all-10170 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.824 Å2
Baniso -1Baniso -2Baniso -3
1--2.16 Å20 Å21.66 Å2
2---0.98 Å20 Å2
3---4.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 0 86 2260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222212
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.962992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0735264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56724.917120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97215391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0491514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021686
X-RAY DIFFRACTIONr_nbd_refined0.2240.2878
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21535
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.29
X-RAY DIFFRACTIONr_mcbond_it2.3231.51330
X-RAY DIFFRACTIONr_mcangle_it4.11122149
X-RAY DIFFRACTIONr_scbond_it5.0293882
X-RAY DIFFRACTIONr_scangle_it7.4184.5843
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 45 -
Rwork0.27 736 -
obs--100 %
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)
10.5006-0.22670.23180.3441-0.17490.18190.0423-0.08710.0674-0.0582-0.0872-0.01130.0119-0.01020.0449-0.0232-0.00260.01470.0018-0.018-0.051528.01431.86216.0852
20.9625-0.04860.16570.10030.01230.361-0.0124-0.0041-0.01160.01280.01240.0064-0.02-0.01150.00010.0079-0.00260.0167-0.01660.0038-0.026428.10531.683716.1051
30.27150.07050.16370.0846-0.0630.51930.0138-0.05120.02410.0289-0.07020.01320.05460.02330.0565-0.0561-0.01350.0132-0.01680.0019-0.02325.1271-4.27711.0072
40.2070.0580.06730.0653-0.05770.14120.013-0.040.00230.0352-0.0118-0.00080.0066-0.0337-0.0011-0.00150.01210.01460.0021-0.004-0.01595.0286-4.41611.0814
50.00520.0042-0.02830.0034-0.0230.1546-0.0724-0.0197-0.02520.03230.07840.04150.0184-0.0787-0.00610.0236-0.0074-0.00590.07530.02520.059714.5171-3.295312.788
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 136
2X-RAY DIFFRACTION2A1 - 136
3X-RAY DIFFRACTION3B3 - 135
4X-RAY DIFFRACTION4B3 - 135
5X-RAY DIFFRACTION5B1 - 230

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