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- PDB-1xkp: Crystal structure of the virulence factor YopN in complex with it... -

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Basic information

Entry
Database: PDB / ID: 1xkp
TitleCrystal structure of the virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB
Components
  • Chaperone protein sycN
  • Chaperone protein yscB
  • putative membrane-bound Yop targeting protein YopN
KeywordsMEMBRANE PROTEIN/chaperon / YopN / Type III secretion / chaperone / SycN / YscB / MEMBRANE PROTEIN-chaperon COMPLEX
Function / homology
Function and homology information


protein secretion by the type III secretion system / protein secretion / negative regulation of protein secretion / cell outer membrane / cell surface / plasma membrane / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #670 / Type III secretion system chaperone SycN / Type III secretion system chaperone YscB / Type III secretion regulator, YopN/LcrE/InvE/MxiC / Hypersensitivity response secretion-like, HrpJ / HrpJ-like domain / 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 - #670 / Type III secretion system chaperone SycN / Type III secretion system chaperone YscB / Type III secretion regulator, YopN/LcrE/InvE/MxiC / Hypersensitivity response secretion-like, HrpJ / HrpJ-like domain / 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
: / Chaperone protein SycN / Outer membrane protein YopN / Chaperone protein YscB
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.7 Å
AuthorsSchubot, F.D. / Jackson, M.W. / Penrose, K.J. / Cherry, S. / Tropea, J.E. / Plano, G.V. / Waugh, D.S.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Three-dimensional structure of a macromolecular assembly that regulates type III secretion in Yersinia pestis.
Authors: Schubot, F.D. / Jackson, M.W. / Penrose, K.J. / Cherry, S. / Tropea, J.E. / Plano, G.V. / Waugh, D.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: A pivotal role for reductive methylation in the de novo crystallization of a ternary complex composed of Yersinia pestis virulence factors YopN, SycN and YscB
Authors: Schubot, F.D. / Waugh, D.S.
History
DepositionSep 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: putative membrane-bound Yop targeting protein YopN
B: Chaperone protein sycN
C: Chaperone protein yscB


Theoretical massNumber of molelcules
Total (without water)57,9053
Polymers57,9053
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-36 kcal/mol
Surface area23180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.718, 60.718, 140.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein putative membrane-bound Yop targeting protein YopN


Mass: 27741.438 Da / Num. of mol.: 1 / Fragment: residues 32-277 / Mutation: deleted N-terminal 31 and C-terminal 16 residues
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: yopN / Plasmid: pDest42 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 3822072, UniProt: P68640*PLUS
#2: Protein Chaperone protein sycN /


Mass: 13770.975 Da / Num. of mol.: 1 / Mutation: P123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: sycN / Plasmid: pDest42 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61380
#3: Protein Chaperone protein yscB / / Yop proteins translocation protein B


Mass: 16392.154 Da / Num. of mol.: 1 / Mutation: C-terminal His-Tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: yscB / Plasmid: pDest42 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q56973
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.97 %

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Data collection

DetectorDate: Nov 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→60.86 Å / Num. obs: 55724

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→60.86 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.392 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -1 / ESU R: 0.114 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24197 2791 5.1 %RANDOM
Rwork0.19839 ---
all0.20059 52879 --
obs0.20059 51811 97.98 %-
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: 33.411 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2---1.32 Å20 Å2
3---2.63 Å2
Refinement stepCycle: LAST / Resolution: 1.7→60.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3773 0 0 179 3952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213830
X-RAY DIFFRACTIONr_bond_other_d0.0020.023694
X-RAY DIFFRACTIONr_angle_refined_deg1.4942.025189
X-RAY DIFFRACTIONr_angle_other_deg1.53138575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69425.179168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97315623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.161524
X-RAY DIFFRACTIONr_chiral_restr0.0960.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
X-RAY DIFFRACTIONr_nbd_refined0.2350.2820
X-RAY DIFFRACTIONr_nbd_other0.1810.23769
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21835
X-RAY DIFFRACTIONr_nbtor_other0.1010.22431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2167
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.27
X-RAY DIFFRACTIONr_mcbond_it1.2591.53073
X-RAY DIFFRACTIONr_mcbond_other0.2471.5970
X-RAY DIFFRACTIONr_mcangle_it1.45923822
X-RAY DIFFRACTIONr_scbond_it2.42731585
X-RAY DIFFRACTIONr_scangle_it3.6564.51367
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 176 -
Rwork0.287 3077 -
obs--79.3 %
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)
13.9942-2.1704-0.40154.7728-0.82710.79680.09990.2106-0.0666-0.1261-0.17960.05060.01190.16130.07970.057-0.02440.004-0.0302-0.0845-0.142945.284-28.64472.924
22.8009-2.16160.06912.53280.05961.6369-0.1548-0.21430.01830.09810.1676-0.00370.113-0.1134-0.0128-0.0029-0.0102-0.0067-0.0228-0.0309-0.135641.453-23.33779.348
32.0077-0.54760.28070.619-0.18360.7883-0.0678-0.0837-0.2383-0.00950.0611-0.03280.0380.02640.0066-0.02290.0280.00660.0405-0.0272-0.06660.3147.3175.558
41.6438-0.0808-0.19884.8972-0.34760.86360.0973-0.0922-0.0793-0.0429-0.0860.3709-0.0455-0.1814-0.0113-0.10790.0422-0.04020.1209-0.0113-0.129226.759-5.91775.74
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA32 - 571 - 26
2X-RAY DIFFRACTION2BB2 - 1212 - 121
3X-RAY DIFFRACTION3AA65 - 26934 - 238
4X-RAY DIFFRACTION4CC2 - 1272 - 127

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