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- PDB-6ejp: Yersinia YscU C-terminal fragment in complex with a synthetic compound -

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Basic information

Entry
Database: PDB / ID: 6ejp
TitleYersinia YscU C-terminal fragment in complex with a synthetic compound
Components(Yop proteins translocation protein ...) x 2
KeywordsTRANSPORT PROTEIN / AUTOCLEAVAGE / TYPE III SECRETION SYSTEM / INHIBITOR
Function / homology
Function and homology information


protein secretion / plasma membrane
Similarity search - Function
secretion proteins EscU / name from scop / Type III exporter system, secretion apparatus protein BsaZ / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-B8E / PHOSPHATE ION / Yop proteins translocation protein U
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsKarlberg, T. / Thorsell, A.G. / Ho, O. / Sunduru, N. / Elofsson, M. / Wolf-Watz, M. / Schuler, H.
CitationJournal: To Be Published
Title: Yersinia YscU C-terminal fragment in complex with a synthetic compound
Authors: Karlberg, T. / Thorsell, A.G. / Ho, O. / Sunduru, N. / Elofsson, M. / Wolf-Watz, M. / Schuler, H.
History
DepositionSep 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Yop proteins translocation protein U
C: Yop proteins translocation protein U
B: Yop proteins translocation protein U
D: Yop proteins translocation protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,59811
Polymers34,7604
Non-polymers8387
Water28816
1
A: Yop proteins translocation protein U
C: Yop proteins translocation protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8767
Polymers17,3802
Non-polymers4965
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Yop proteins translocation protein U
D: Yop proteins translocation protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7224
Polymers17,3802
Non-polymers3422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.740, 69.650, 242.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11C-502-

PO4

21C-502-

PO4

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Components

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Yop proteins translocation protein ... , 2 types, 4 molecules ABCD

#1: Protein Yop proteins translocation protein U


Mass: 6832.867 Da / Num. of mol.: 2 / Fragment: N-terminal fragment, UNP residues 211-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: yscU, YPCD1.47, y5031, y0034, YP_pCD36 / Plasmid: PGEX / Details (production host): N-terminal GST tag / Production host: Escherichia coli (E. coli) / References: UniProt: P69986
#2: Protein Yop proteins translocation protein U


Mass: 10547.121 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, UNP residues 264-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: yscU, YPCD1.47, y5031, y0034, YP_pCD36 / Plasmid: PGEX / Details (production host): N-terminal GST tag / Production host: Escherichia coli (E. coli) / References: UniProt: P69986

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Non-polymers , 5 types, 23 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-B8E / methyl 2-(5-methyl-2-phenyl-1,3-thiazol-4-yl)ethanoate


Mass: 247.313 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13NO2S
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8 M potassium dihydrogen phosphate, 0.8 M disodium hydrogen phosphate, 0.1 M Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Oct 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.48→44.8 Å / Num. obs: 16706 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Biso Wilson estimate: 68.39 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.121 / Net I/σ(I): 15.1
Reflection shellResolution: 2.48→2.63 Å / Redundancy: 14 % / Rmerge(I) obs: 0.877 / Num. unique obs: 2613 / CC1/2: 0.9 / % possible all: 98.6

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JLI

2jli


Resolution: 2.48→23.39 Å / Cor.coef. Fo:Fc: 0.9175 / Cor.coef. Fo:Fc free: 0.8956 / SU R Cruickshank DPI: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.305 / SU Rfree Blow DPI: 0.233 / SU Rfree Cruickshank DPI: 0.237
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 832 5 %RANDOM
Rwork0.2144 ---
obs0.2162 16636 99.9 %-
Displacement parametersBiso mean: 68.06 Å2
Baniso -1Baniso -2Baniso -3
1--15.9696 Å20 Å20 Å2
2---2.0355 Å20 Å2
3---18.0051 Å2
Refine analyzeLuzzati coordinate error obs: 0.385 Å
Refinement stepCycle: 1 / Resolution: 2.48→23.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 51 16 2391
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0122412HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.23246HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1161SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes79HARMONIC2
X-RAY DIFFRACTIONt_gen_planes331HARMONIC5
X-RAY DIFFRACTIONt_it2412HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion3.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion310SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2648SEMIHARMONIC4
LS refinement shellResolution: 2.48→2.65 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2785 147 5 %
Rwork0.2487 2792 -
all0.2501 2939 -
obs--99.9 %
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)
10.5668-0.2205-0.51551.54411.21433.98390.10760.1458-0.13730.0574-0.17040.1670.1471-0.06320.0628-0.1846-0.0286-0.0001-0.09270.0184-0.0798-13.0264-7.854656.9018
21.0709-0.0206-0.85940.4465-0.0832.1784-0.1269-0.0084-0.1164-0.01640.19850.1296-0.0137-0.3598-0.07150.01980.0076-0.0218-0.11380.0138-0.1303-22.15521.72014.8933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|211-263 }A211 - 263
2X-RAY DIFFRACTION1{ C|364-450 }C364 - 450
3X-RAY DIFFRACTION2{ B|213-263 }B213 - 263
4X-RAY DIFFRACTION2{ D|364-453 }D364 - 453

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