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- PDB-1ttw: Crystal structure of the Yersinia Pestis type III secretion chape... -

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Basic information

Entry
Database: PDB / ID: 1ttw
TitleCrystal structure of the Yersinia Pestis type III secretion chaperone SycH in complex with a stable fragment of YscM2
Components
  • YscM2
  • secretion chaperone
KeywordsCHAPERONE / type III secretion
Function / homology
Function and homology information


protein secretion by the type III secretion system / protein tyrosine phosphatase activity
Similarity search - Function
Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Protein-tyrosine phosphatase, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / YopH targeting protein / YopH targeting protein / YscM2
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.38 Å
AuthorsPhan, J. / Tropea, J.E. / Waugh, D.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the Yersinia pestis type III secretion chaperone SycH in complex with a stable fragment of YscM2.
Authors: Phan, J. / Tropea, J.E. / Waugh, D.S.
History
DepositionJun 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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: secretion chaperone
B: YscM2


Theoretical massNumber of molelcules
Total (without water)21,9952
Polymers21,9952
Non-polymers00
Water73941
1
A: secretion chaperone
B: YscM2

A: secretion chaperone
B: YscM2


Theoretical massNumber of molelcules
Total (without water)43,9904
Polymers43,9904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+2/31
Buried area5140 Å2
ΔGint-45 kcal/mol
Surface area13090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.664, 63.664, 162.263
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-155-

HOH

21A-164-

HOH

31A-169-

HOH

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Components

#1: Protein secretion chaperone


Mass: 15454.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7ARG9, UniProt: Q7BTX0*PLUS
#2: Protein YscM2


Mass: 6540.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / References: GenBank: 28373010, UniProt: Q93KQ4*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.6
Details: 1.8 M ammonium sulphate, 200 mM magnesium acetate, 100 mM CAPSO, 2% dioxane, 1.6 mM CHAPS, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98397 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 22, 2003
RadiationMonochromator: Insertion Device / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98397 Å / Relative weight: 1
ReflectionResolution: 2.38→25 Å / Num. all: 9196 / Num. obs: 7916 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13 % / Biso Wilson estimate: 66.026 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.9
Reflection shellResolution: 2.38→2.48 Å / Redundancy: 10 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4 / Num. unique all: 888 / % possible all: 67.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.38→25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.627 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.31 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29219 388 4.7 %RANDOM
Rwork0.24312 ---
obs0.24541 7916 98.83 %-
all-9196 --
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: 67.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.3 Å20 Å2
2--0.61 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.38→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms993 0 0 41 1034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0440.0211008
X-RAY DIFFRACTIONr_bond_other_d0.0030.02944
X-RAY DIFFRACTIONr_angle_refined_deg3.5181.9391381
X-RAY DIFFRACTIONr_angle_other_deg1.48432171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.7045136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1930.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021140
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02191
X-RAY DIFFRACTIONr_nbd_refined0.2850.2262
X-RAY DIFFRACTIONr_nbd_other0.2780.21145
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1280.2699
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2760.248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5140.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.8971.5683
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.37621076
X-RAY DIFFRACTIONr_scbond_it4.593325
X-RAY DIFFRACTIONr_scangle_it7.1284.5305
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.38→2.441 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.372 37
Rwork0.295 563

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