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- PDB-2jlj: Crystal Structure of the cytoplasmic domain of Yersinia pestis Ys... -

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Basic information

Entry
Database: PDB / ID: 2jlj
TitleCrystal Structure of the cytoplasmic domain of Yersinia pestis YscU N263A P264A mutant
ComponentsYOP PROTEINS TRANSLOCATION PROTEIN U
KeywordsPROTEIN TRANSPORT / CELL MEMBRANE / TRANSMEMBRANE / YERSINIA PESITS / TYPE III SECRETION SYSTEM / MEMBRANE / VIRULENCE / TRANSPORT
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
Yop proteins translocation protein U
Similarity search - Component
Biological speciesYERSINIA PESTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsLountos, G.T. / Austin, B.P. / Nallamsetty, S. / Waugh, D.S.
CitationJournal: Protein Sci. / Year: 2009
Title: Atomic Resolution Structure of the Cytoplasmic Domain of Yersinia Pestis Yscu, a Regulatory Switch Involved in Type III Secretion.
Authors: Lountos, G.T. / Austin, B.P. / Nallamsetty, S. / Waugh, D.S.
History
DepositionSep 9, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YOP PROTEINS TRANSLOCATION PROTEIN U


Theoretical massNumber of molelcules
Total (without water)16,8811
Polymers16,8811
Non-polymers00
Water3,099172
1
A: YOP PROTEINS TRANSLOCATION PROTEIN U

A: YOP PROTEINS TRANSLOCATION PROTEIN U


Theoretical massNumber of molelcules
Total (without water)33,7632
Polymers33,7632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area1960 Å2
ΔGint-11.4 kcal/mol
Surface area14120 Å2
MethodPQS
Unit cell
Length a, b, c (Å)66.041, 66.041, 70.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2115-

HOH

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Components

#1: Protein YOP PROTEINS TRANSLOCATION PROTEIN U / YSCU


Mass: 16881.467 Da / Num. of mol.: 1 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 211-354 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: PSN2006 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P69986
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 263 TO ALA ENGINEERED RESIDUE IN CHAIN A, PRO 264 TO ALA

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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: 2.5 Å3/Da / Density % sol: 49.8 % / Description: NONE
Crystal growpH: 7
Details: 100 MM HEPES PH 7, 1 M SODIUM MALONATE PH 7, 0.75 M SODIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 37461 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.2
Reflection shellResolution: 1.3→1.34 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.6 / % possible all: 66.5

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Processing

Software
NameVersionClassification
REFMAC5.4.0057refinement
HKL-3000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.3→48.28 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.844 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1877 5 %RANDOM
Rwork0.219 ---
obs0.22 35584 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.3→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 0 172 1088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022967
X-RAY DIFFRACTIONr_bond_other_d0.0020.02670
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9551323
X-RAY DIFFRACTIONr_angle_other_deg1.06131637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4145126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44522.95544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1415173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3811510
X-RAY DIFFRACTIONr_chiral_restr0.1170.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02196
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0041.5594
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7842971
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6963373
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2674.5346
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: 1.3→1.34 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.39 88
Rwork0.417 1885
Refinement TLS params.Method: refined / Origin x: 19.291 Å / Origin y: -12.468 Å / Origin z: -5.23 Å
111213212223313233
T-0.0883 Å2-0.0059 Å20.0021 Å2--0.1174 Å20.0048 Å2---0.0314 Å2
L1.0859 °20.0801 °20.2489 °2-1.355 °20.1349 °2--1.0454 °2
S0.009 Å °-0.1062 Å °-0.0519 Å °0.1977 Å °-0.0202 Å °0.0012 Å °0.0288 Å °-0.1011 Å °0.0112 Å °

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