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- PDB-2bsi: Crystal structure of the type III secretion chaperone SycT from Y... -

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Basic information

Entry
Database: PDB / ID: 2bsi
TitleCrystal structure of the type III secretion chaperone SycT from Yersinia enterocolitica (crystal form 1)
ComponentsYOPT CHAPERONE SYCT
KeywordsCHAPERONE / TYPE III SECRETION / YERSINIA / EFFECTOR / YOPT
Function / homologyTir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / protein secretion by the type III secretion system / 2-Layer Sandwich / Alpha Beta / Chaperone protein SycT / Chaperone protein SycT
Function and homology information
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsButtner, C.R. / Cornelis, G.R. / Heinz, D.W. / Niemann, H.H.
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal Structure of Yersinia Enterocolitica Type III Secretion Chaperone Syct.
Authors: Buttner, C.R. / Cornelis, G.R. / Heinz, D.W. / Niemann, H.H.
History
DepositionMay 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YOPT CHAPERONE SYCT
B: YOPT CHAPERONE SYCT


Theoretical massNumber of molelcules
Total (without water)29,2742
Polymers29,2742
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.539, 63.090, 74.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99997, -0.00234, -0.0076), (0.0021, -0.99949, 0.03173), (-0.00767, 0.03172, 0.99947)
Vector: -25.9313, -11.24665, 0.12778)

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Components

#1: Protein YOPT CHAPERONE SYCT


Mass: 14636.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Strain: W22703
Description: YERSINIA ENTEROCOLITICA VIRULENCE PLASMID PYVE227
Variant: SEROTYPE O\:9 / Plasmid: PET-M-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O85243, UniProt: P0C2V9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1.6 M AMMONIUM SULFATE, 0.1 M CAPS PH 10.5, 150 MM LITHIUM SULFATE HANGING-DROP VAPOR DIFFUSION AT 4 DEG C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→48.1 Å / Num. obs: 16331 / % possible obs: 98.4 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.08 / Rsym value: 0.07 / Net I/σ(I): 12.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.32 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BSH

2bsh


Resolution: 2.01→48.11 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.329 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 821 5 %RANDOM
Rwork0.203 ---
obs0.206 15511 98.3 %-
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: 40.97 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å20 Å2
2---2.08 Å20 Å2
3---4.37 Å2
Refinement stepCycle: LAST / Resolution: 2.01→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 0 123 1999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212013
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0711.9192745
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1535246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42425.726117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.0115346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.833158
X-RAY DIFFRACTIONr_chiral_restr0.150.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021596
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.2911
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21375
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.331.51254
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.95721921
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0013914
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8894.5824
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 65 -
Rwork0.233 1099 -
obs--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)
17.14892.36331.43814.39010.16721.10750.0439-0.1441-0.38170.1416-0.04990.2140.0394-0.08670.006-0.0769-0.00530.0274-0.1301-0.0044-0.2515-20.863-14.168-15.275
25.89581.5562-0.48754.7291-0.05141.5335-0.0611-0.12120.27860.08940.043-0.4276-0.0760.02150.018-0.087-0.0035-0.0346-0.15970.0067-0.2362-4.7172.5-15.503
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 113
2X-RAY DIFFRACTION2B0 - 113

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