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- PDB-2v5g: Crystal structure of the mutated N263A YscU C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2v5g
TitleCrystal structure of the mutated N263A 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
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 / Derived calculations ...Data collection / Derived calculations / 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 / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

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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)17,0302
Polymers16,9951
Non-polymers351
Water93752
1
A: YSCU
hetero molecules

A: YSCU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0614
Polymers33,9902
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area1880 Å2
ΔGint-10.8 kcal/mol
Surface area14190 Å2
MethodPQS
Unit cell
Length a, b, c (Å)66.297, 66.297, 68.500
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-2041-

HOH

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Components

#1: Protein YSCU


Mass: 16994.943 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.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 263 TO ALA
Has protein modificationY

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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: 2.23 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 3UL 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: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97854
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 10836 / % possible obs: 99.9 % / Observed criterion σ(I): 2.2 / Redundancy: 13.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.1
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2→29.84 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.549 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.164 / 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
Rfree0.253 328 3 %RANDOM
Rwork0.221 ---
obs0.222 10436 99.7 %-
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: 30.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 1 52 1029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221054
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.9651435
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2635132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44322.69252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97515201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9061513
X-RAY DIFFRACTIONr_chiral_restr0.1140.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02805
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.2487
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.2716
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0492660
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.05231031
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3982.5458
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2983399
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.219 18
Rwork0.233 734

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