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- PDB-2vgy: Crystal structure of the Yersinia enterocolitica Type III Secreti... -

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Basic information

Entry
Database: PDB / ID: 2vgy
TitleCrystal structure of the Yersinia enterocolitica Type III Secretion Translocator Chaperone SycD (alternative dimer)
ComponentsCHAPERONE SYCD
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: 2.6 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 / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
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
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


Theoretical massNumber of molelcules
Total (without water)16,7441
Polymers16,7441
Non-polymers00
Water50428
1
A: CHAPERONE SYCD

A: CHAPERONE SYCD


Theoretical massNumber of molelcules
Total (without water)33,4882
Polymers33,4882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area1420 Å2
ΔGint-16 kcal/mol
Surface area17640 Å2
MethodPQS
Unit cell
Length a, b, c (Å)90.638, 90.638, 54.205
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsACCORDING TO THE AUTHOR THE BIOLOGICAL UNIT IS A HOMODIMER, WHERE MONOMERS ARE RELATED BY TWO-FOLD CRYSTALLOGRAPHIC ROTATIONAL SYMMETRY (ALTERNATIVE DIMER ASSEMBLY = DIMER 3)

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Components

#1: Protein CHAPERONE SYCD


Mass: 16744.148 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-163 / Mutation: YES
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 94 TO GLU ENGINEERED RESIDUE IN CHAIN A, TYR 95 TO GLU
Nonpolymer detailsN-DIMETHYL-LYSINE (MLY): REDUCTIVE METHYLATION
Sequence detailsSYCD RESIDUES 21-163. FIVE ADDITIONAL RESIDUES AT THE N- TERMINUS DUE TO PRESCISSION PROTEASE ...SYCD RESIDUES 21-163. FIVE ADDITIONAL RESIDUES AT THE N- TERMINUS DUE TO PRESCISSION PROTEASE CLEAVAGE. DOUBLE-SITE MUTATION S94E_Y95E.

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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: 3.92 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growTemperature: 277 K
Details: 40% PEG400, 5% PEG3350, 0.1M SODIUM ACTATE PH 5.5 AT 4 DEGREES CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→39.2 Å / Num. obs: 8163 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.12 / Rsym value: 0.11 / Net I/σ(I): 20
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.56 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VGX

2vgx


Resolution: 2.6→39.2474 Å / Stereochemistry target values: ML
Details: TLS REFINEMENT CARRIED OUT IN PHENIX. ANISOU RECORDS CONTAIN THE ANISOTROPIC B-FACTOR THAT IS THE TOTAL B-FACTOR (B_TLS + B_INDIVIDUAL). ATOM RECORDS CONTAINISOTROPIC EQUIVALENTS OF THE ...Details: TLS REFINEMENT CARRIED OUT IN PHENIX. ANISOU RECORDS CONTAIN THE ANISOTROPIC B-FACTOR THAT IS THE TOTAL B-FACTOR (B_TLS + B_INDIVIDUAL). ATOM RECORDS CONTAINISOTROPIC EQUIVALENTS OF THE TOTAL B-FACTOR THAT IS THE MEAN OF THE ANISOU MATRIX TRACE DIVIDED BY 10000 AND MULTIPLIED BY 8*PI^2. INDIVIDUAL B-FACTORS ARE OBTAINED BY SUBTRACTING THE TLS COMPONENT (B_TLS), CALCULATED BY THE TLS RECORDS FROM THE PDB FILE HEADER, FROM THE TOTAL B-FACTORS (ANISOU RECORDS).
RfactorNum. reflection% reflection
Rfree0.2343 407 5 %
Rwork0.2134 --
obs-8120 99.42 %
Refinement stepCycle: LAST / Resolution: 2.6→39.2474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1069 0 0 28 1097
Refinement TLS params.Method: refined / Origin x: 34.5442 Å / Origin y: -24.9209 Å / Origin z: 14.3549 Å
111213212223313233
T0.2012 Å2-0.0578 Å20.0511 Å2-0.1613 Å20.0311 Å2--0.121 Å2
L1.4691 °20.4534 °2-0.5932 °2-0.3514 °2-0.1603 °2--0.7189 °2
S0.2608 Å °-0.0368 Å °0.2026 Å °0.1606 Å °-0.013 Å °0.1125 Å °0.078 Å °-0.0209 Å °-0.08 Å °
Refinement TLS groupSelection details: CHAIN A

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