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- PDB-1jya: Crystal Structure of SycE -

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Basic information

Entry
Database: PDB / ID: 1jya
TitleCrystal Structure of SycE
ComponentsYOPE regulator
KeywordsCHAPERONE / SPECIFIC CHAPERONE / TYPE III SECRETION
Function / homology
Function and homology information


protein secretion by the type III secretion system
Similarity search - Function
Type III secretion chaperone SycE / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
YopE regulator / YopE regulator
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.74 Å
AuthorsGhosh, P. / Birtalan, S.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of the Yersinia type III secretory system chaperone SycE.
Authors: Birtalan, S. / Ghosh, P.
History
DepositionSep 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.temp
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE THE SEQUENCE OF THE SYCE PROTEIN, CHAINS A-B, MATCHES SWISS PROT ENTRY P31491, WHOSE ...SEQUENCE THE SEQUENCE OF THE SYCE PROTEIN, CHAINS A-B, MATCHES SWISS PROT ENTRY P31491, WHOSE SOURCE IS YERSINIA PESTIS. THE SOURCE OF THE SYCE PROTEIN IN THIS ENTRY IS YERSINIA PSEUDOTUBERCULOSIS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YOPE regulator
B: YOPE regulator


Theoretical massNumber of molelcules
Total (without water)29,6002
Polymers29,6002
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-21 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.000, 75.190, 137.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

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Components

#1: Protein YOPE regulator / yopE chaperone sycE


Mass: 14800.232 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: syce / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31491, UniProt: Q663P0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 50 %
Description: 25% PEG 4000, 0.3M MGCL2,0.1M TRIS, PH 8.5, 0.001M DTT
Crystal growpH: 8.5 / Details: pH 8.5, temperature 100K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
125 %(w/v)PEG40001reservoir
2300 mM1reservoirMgCl2
3100 mMTris1reservoirpH8.5
41 mMdithiothreitol1reservoir
510 mMTris1droppH8.0
61 mMdithiothreitol1drop
740 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97918
DetectorDetector: CCD / Date: Mar 30, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.74→20 Å / Num. obs: 46896 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 19
Reflection shellResolution: 1.74→1.77 Å / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.365 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 20 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.74→20 Å / Isotropic thermal model: atomic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2376 5 %random 5%
Rwork0.236 ---
obs-46896 93.6 %-
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.023 Å20 Å20 Å2
2--0.319 Å20 Å2
3---1.703 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.74→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 0 133 2028
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0048
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_dihedral_angle_d23.01
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it4.0365
X-RAY DIFFRACTIONc_mcangle_it5.8187
X-RAY DIFFRACTIONc_scbond_it5.3497
X-RAY DIFFRACTIONc_scangle_it7.5429
LS refinement shellResolution: 1.74→1.8 Å
RfactorNum. reflection% reflection
Rfree0.369 207 4.4 %
Rwork0.323 4487 -
obs-4487 99.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CIS_PEPTIDE.PARAM
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.01
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69
LS refinement shell
*PLUS
Lowest resolution: 1.77 Å

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