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

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Basic information

Entry
Database: PDB / ID: 2bsh
TitleCrystal structure of the type III secretion chaperone SycT from Yersinia enterocolitica (crystal form 2)
ComponentsSYCT
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 / SAD / Resolution: 1.9 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 1.0Aug 15, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: SECONDARY STRUCTURE ASSIGNED BY STRIDE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SYCT
B: SYCT


Theoretical massNumber of molelcules
Total (without water)29,2742
Polymers29,2742
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.040, 92.040, 55.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.87503, 0.43364, 0.21513), (0.43477, -0.89944, 0.04459), (0.21283, 0.05451, -0.97557)
Vector: 2.79374, -1.00649, -22.34988)

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Components

#1: Protein 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.: 139 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIT IS A SPECIFIC CHAPERONE FOR YOPT
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: 2.21 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1.8 M AMMONIUM SULFATE, 0.1 M SODIUM BICARBONATE PH 10.5, 50 MM MAGNESIUM CHLORIDE HANGING-DROP VAPOR DIFFUSION AT 4 CELSIUS DEGREE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97957
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.9→79.81 Å / Num. obs: 21134 / % possible obs: 99.5 % / Redundancy: 11.2 % / Net I/σ(I): 16.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.53 / Rsym value: 0.07 / % possible all: 96.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
SHELXphasing
CDEphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: SAD / Resolution: 1.9→79.81 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.12 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1085 5.1 %RANDOM
Rwork0.174 ---
obs0.176 20049 100 %-
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: 23.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0.37 Å20 Å2
2---0.73 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→79.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 0 139 2080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211988
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.9192700
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0115234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97125.948116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93615335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.209156
X-RAY DIFFRACTIONr_chiral_restr0.1620.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021561
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.3939
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.51363
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.5251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.357
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.515
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.28921204
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.38831884
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7512907
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6463816
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: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 67 -
Rwork0.2 1461 -
obs--99.87 %
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)
14.7273-0.45340.37493.3314-0.87562.34210.04790.1269-0.07770.1384-0.13780.048-0.06910.0120.08990.051-0.02620.03490.0183-0.00090.048457.620213.8417-2.1721
215.5612-0.10750.46771.4857-0.3131.6413-0.08270.586-0.47790.2421-0.00350.0968-0.15720.12140.08620.1201-0.06440.02580.0834-0.03760.038355.746616.66123.4244
36.22611.6489-0.55612.3028-1.80572.64020.0867-0.7161-0.4237-0.235-0.4118-0.6488-0.29650.33770.3252-0.043-0.05980.08890.15210.13090.178981.122921.3229-11.3036
43.63821.1483-1.24193.8104-1.37872.19240.0262-0.007-0.13380.0021-0.1313-0.10470.0298-0.02240.10520.0186-0.01190.02940.00490.01290.00662.417812.8547-9.0314
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 93
2X-RAY DIFFRACTION2A94 - 122
3X-RAY DIFFRACTION3B-2 - 33
4X-RAY DIFFRACTION4B34 - 114

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