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- PDB-2w0r: Crystal structure of the mutated N263D YscU C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2w0r
TitleCrystal structure of the mutated N263D YscU C-terminal domain
ComponentsYSCU
KeywordsMEMBRANE PROTEIN / PLASMID / AUTOCLEAVAGE / RECOGNITION PROTEIN / TYPE III SECRETION SYSTEM
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 ENTEROCOLITICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWiesand, U. / Sorg, I. / Amstutz, M. / Wagner, S. / Van Den Heuvel, J. / Luehrs, T. / Cornelis, G.R. / Heinz, D.W.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Structure of the Type III Secretion Recognition Protein Yscu from Yersinia Enterocolitica
Authors: Wiesand, U. / Sorg, I. / Amstutz, M. / Wagner, S. / Van Den Heuvel, J. / Luehrs, T. / Cornelis, G.R. / Heinz, D.W.
#1: Journal: J.Bacteriol. / Year: 1994
Title: Yscu, a Yersinia Enterocolitica Inner Membrane Protein Involved in Yop Secretion.
Authors: Allaoui, A. / Woestyn, S. / Sluiters, C. / Cornelis, G.R.
History
DepositionOct 6, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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: YSCU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9223
Polymers16,8511
Non-polymers712
Water2,396133
1
A: YSCU
hetero molecules

A: YSCU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8456
Polymers33,7032
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2010 Å2
ΔGint-9.3 kcal/mol
Surface area15250 Å2
MethodPQS
Unit cell
Length a, b, c (Å)66.473, 66.473, 68.113
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-2098-

HOH

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Components

#1: Protein YSCU


Mass: 16851.371 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 211-354 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Strain: W22703 / Plasmid: PGEX-6-P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER DE3 / References: UniProt: Q56844
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 263 TO ASP

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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: 2.24 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: HANGING DROP METHOD USING 3 UL OF A 8 MG/ML PROTEIN SOLUTION MIXED WITH 3 UL RESERVOIR BUFFER (1.6 M (NH4)2SO4, 0.2 M NACL, 0.1 M HEPES PH 7.5) IN THE DROPLET.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.55→10 Å / Num. obs: 21871 / % possible obs: 96.7 % / Observed criterion σ(I): 4.8 / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.4
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V5G

2v5g


Resolution: 1.55→10 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.354 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MISSING RESIDUES 211-221 AND 343-354 DUE TO WEAK DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 700 3.2 %RANDOM
Rwork0.201 ---
obs0.202 21138 96.5 %-
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: 21.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms999 0 2 133 1134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221142
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9721571
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5245155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74923.10358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27115230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6291514
X-RAY DIFFRACTIONr_chiral_restr0.0990.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02878
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.2531
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2870.2802
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0890.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6522710
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.38331114
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.942510
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.843440
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: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.209 57
Rwork0.215 1544

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