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- PDB-1xl3: Complex structure of Y.pestis virulence Factors YopN and TyeA -

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Basic information

Entry
Database: PDB / ID: 1xl3
TitleComplex structure of Y.pestis virulence Factors YopN and TyeA
Components
  • Secretion control protein
  • protein type A
KeywordsCELL INVASION / yopN / TyeA / Yersinia pestis / type III secretion
Function / homology
Function and homology information


protein secretion by the type III secretion system / negative regulation of protein secretion / cell outer membrane / cell surface
Similarity search - Function
Monooxygenase - #80 / Type III secretion system effector delivery regulator TyeA / TyeA / TyeA superfamily / Type III secretion system effector delivery regulator TyeA-related / Type III secretion regulator, YopN/LcrE/InvE/MxiC / Hypersensitivity response secretion-like, HrpJ / HrpJ-like domain / Monooxygenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Protein TyeA / Outer membrane protein YopN / Protein TyeA
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 30, 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: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Secretion control protein
B: Secretion control protein
C: protein type A
D: protein type A


Theoretical massNumber of molelcules
Total (without water)70,9744
Polymers70,9744
Non-polymers00
Water3,243180
1
A: Secretion control protein
C: protein type A


Theoretical massNumber of molelcules
Total (without water)35,4872
Polymers35,4872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-25 kcal/mol
Surface area16700 Å2
MethodPISA
2
B: Secretion control protein
D: protein type A


Theoretical massNumber of molelcules
Total (without water)35,4872
Polymers35,4872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-26 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.172, 170.724, 55.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Secretion control protein / Yop4b / LcrE


Mass: 24642.873 Da / Num. of mol.: 2 / Mutation: residues 76-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: yopN, lcrE / 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 protein type A


Mass: 10844.321 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: tyeA / Plasmid: pDest42 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P16161, UniProt: P69968*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.75 Å3/Da / Density % sol: 55.21 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 40229

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XKP chain A residues 76-269

1xkp


Resolution: 2.2→84.51 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 13.207 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -1 / ESU R: 0.236 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25036 1949 5.1 %RANDOM
Rwork0.19164 ---
all0.19461 38535 --
obs0.19461 36265 94.11 %-
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: 40.988 Å2
Baniso -1Baniso -2Baniso -3
1--3.85 Å20 Å20 Å2
2---0.62 Å20 Å2
3---4.47 Å2
Refinement stepCycle: LAST / Resolution: 2.2→84.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 0 180 4878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214778
X-RAY DIFFRACTIONr_bond_other_d0.0020.024445
X-RAY DIFFRACTIONr_angle_refined_deg1.772.0086450
X-RAY DIFFRACTIONr_angle_other_deg0.897310335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7125579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44925.314239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.42515754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1391528
X-RAY DIFFRACTIONr_chiral_restr0.10.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025253
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02909
X-RAY DIFFRACTIONr_nbd_refined0.2240.21240
X-RAY DIFFRACTIONr_nbd_other0.1950.24545
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22365
X-RAY DIFFRACTIONr_nbtor_other0.0980.22804
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0450.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.3161.53707
X-RAY DIFFRACTIONr_mcbond_other0.2271.51188
X-RAY DIFFRACTIONr_mcangle_it1.58724657
X-RAY DIFFRACTIONr_scbond_it2.7432096
X-RAY DIFFRACTIONr_scangle_it4.2934.51793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 130 -
Rwork0.224 2420 -
obs--85.97 %
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)
11.67410.9047-0.1191.95140.52790.8722-0.17810.2045-0.378-0.08050.1292-0.34560.1145-0.17290.04890.0734-0.03770.0555-0.0238-0.0327-0.098363.2437.5349.123
21.32051.19160.18492.3643-0.13420.0962-0.1070.13380.1449-0.19630.13610.10720.00350.0271-0.02910.0986-0.01630.0223-0.002-0.0229-0.124164.20697.85243.489
32.7445-0.3649-1.55313.84810.44973.1221-0.12730.0175-0.15110.0005-0.00130.46060.1862-0.0010.12860.0180.0032-0.0285-0.10130.0088-0.086849.4663.36753.653
42.545-0.8944-0.29522.21810.99241.5339-0.0813-0.31870.140.15040.1174-0.14610.0926-0.0498-0.03610.07750.0323-0.03380.0512-0.0593-0.201464.45570.43969.049
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA78 - 2833 - 208
2X-RAY DIFFRACTION2BB78 - 2833 - 208
3X-RAY DIFFRACTION3CC2 - 862 - 86
4X-RAY DIFFRACTION4DD2 - 862 - 86

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