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- PDB-2vgx: Structure of the Yersinia enterocolitica Type III Secretion Trans... -

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Basic information

Entry
Database: PDB / ID: 2vgx
TitleStructure of the Yersinia enterocolitica Type III Secretion Translocator Chaperone SycD
Components(CHAPERONE SYCD) x 2
KeywordsCHAPERONE / ALTERNATIVE DIMER ASSEMBLY / SYCD / TETRATRICOPEPTIDE REPEAT / TYPE III SECRETION
Function / homology
Function and homology information


Tetratricopeptide TPR-3 / Tetratricopeptide repeat / Type III secretion system, low calcium response, chaperone LcrH/SycD, subgroup / Type III secretion system, low calcium response, chaperone LcrH/SycD / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsButtner, C.R. / Sorg, I. / Cornelis, G.R. / Heinz, D.W. / Niemann, H.H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of the Yersinia Enterocolitica Type III Secretion Chaperone Sycd
Authors: Buttner, C.R. / Sorg, I. / Cornelis, G.R. / Heinz, D.W. / Niemann, H.H.
History
DepositionNov 16, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHAPERONE SYCD
B: CHAPERONE SYCD


Theoretical massNumber of molelcules
Total (without water)33,3912
Polymers33,3912
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-16.7 kcal/mol
Surface area18220 Å2
MethodPQS
2
A: CHAPERONE SYCD
B: CHAPERONE SYCD

A: CHAPERONE SYCD
B: CHAPERONE SYCD


Theoretical massNumber of molelcules
Total (without water)66,7824
Polymers66,7824
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4980 Å2
ΔGint-63.3 kcal/mol
Surface area32710 Å2
MethodPQS
Unit cell
Length a, b, c (Å)107.247, 32.979, 96.731
Angle α, β, γ (deg.)90.00, 122.34, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.52427, -0.17018, 0.83437), (-0.11921, -0.98485, -0.12596), (0.84317, -0.03343, -0.53661)
Vector: 3.39018, -4.65049, -8.92715)

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Components

#1: Protein CHAPERONE SYCD


Mass: 16655.039 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria)
Description: YERSINIA ENTEROCOLITICA VIRULENCE PLASMID PYVE227 FROM STRAIN W22703
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O87496
#2: Protein CHAPERONE SYCD


Mass: 16736.174 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria)
Description: YERSINIA ENTEROCOLITICA VIRULENCE PLASMID PYVE227 FROM STRAIN W22703
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O87496
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsN-DIMETHYL-LYSINE (MLY): REDUCTIVE METHYLATION
Sequence detailsSYCD RESIDUES 21-163. FIVE ADDITIONAL RESIDUES AT THE N- TERMINUS DUE TO PRESCISSION PROTEASE CLEAVAGE

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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: 43 % / Description: MR SEARCH MODEL WAS PREPARED AS MIXED MODEL
Crystal growTemperature: 277 K
Details: 0.1M TRI-SODIUM CITRATE, 20% PEG 4000, 20% 2-PROPANOL AT 4 DEGREES CELSIUS

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID23-110.97925
SYNCHROTRONEMBL/DESY, HAMBURG X1221.2781
Detector
TypeIDDetectorDate
ADSC CCD1CCDFeb 15, 2007
2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
21.27811
ReflectionResolution: 1.95→45.3 Å / Num. obs: 21282 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.1 / Net I/σ(I): 13.1
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.41 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FO7

2fo7


Resolution: 1.95→45.31 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / SU B: 3.306 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1065 5 %RANDOM
Rwork0.175 ---
obs0.178 20217 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å2-0.13 Å2
2--0.2 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 0 137 2342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212248
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4432.0093028
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.395277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.96724.857105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74315328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.81158
X-RAY DIFFRACTIONr_chiral_restr0.1060.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021744
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.2949
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21549
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.01421421
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.99832177
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4392929
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5423851
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: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 79
Rwork0.201 1484

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