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- PDB-4am9: CRYSTAL STRUCTURE OF THE YERSINIA ENTEROCOLITICA TYPE III SECRETI... -

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Basic information

Entry
Database: PDB / ID: 4am9
TitleCRYSTAL STRUCTURE OF THE YERSINIA ENTEROCOLITICA TYPE III SECRETION CHAPERONE SYCD IN COMPLEX WITH A PEPTIDE OF THE TRANSLOCATOR YOPD
Components
  • CHAPERONE SYCD
  • YOP EFFECTOR YOPD
KeywordsCHAPERONE / CHAPERONE BINDING DOMAIN / CHAPERONE PEPTIDE COMPLEX / PATHOGENICTIY FACTOR / TRANSLOCATOR / TETRATRICOPEPTIDE REPEAT / TPR / T3SS / VIRULENCE FACTOR
Function / homology
Function and homology information


YopD-like / YopD protein / 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
(R,R)-2,3-BUTANEDIOL / Chaperone SycD / Protein YopD / Translocator protein
Similarity search - Component
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSchreiner, M. / Niemann, H.H.
CitationJournal: Bmc Struct.Biol. / Year: 2012
Title: Crystal Structure of the Yersinia Enterocolitica Type III Secretion Chaperone Sycd in Complex with a Peptide of the Minor Translocator Yopd
Authors: Schreiner, M. / Niemann, H.H.
History
DepositionMar 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Other
Revision 1.2Mar 6, 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 1.3Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHAPERONE SYCD
B: YOP EFFECTOR YOPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2058
Polymers17,6582
Non-polymers5476
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-15.5 kcal/mol
Surface area8320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.369, 106.369, 51.998
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CHAPERONE SYCD


Mass: 16492.762 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Strain: W22703
Description: YERSINIA ENTEROCOLITICA VIRULENCE PLASMID PYVE227 FROM STRAIN W22703
Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): CODONPLUS RIL / References: UniProt: O87496
#2: Protein/peptide YOP EFFECTOR YOPD


Mass: 1165.358 Da / Num. of mol.: 1 / Fragment: RESIDUES 56-65 / Source method: obtained synthetically / Source: (synth.) YERSINIA ENTEROCOLITICA (bacteria) / References: UniProt: Q9R2G2, UniProt: P37132*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIVE ADDITIONAL N-TERMINAL RESIDUES DUE TO PRESCISSION PROTEASE CLEAVAGE SYNTHETIC PEPTIDE (CHAIN B) ...FIVE ADDITIONAL N-TERMINAL RESIDUES DUE TO PRESCISSION PROTEASE CLEAVAGE SYNTHETIC PEPTIDE (CHAIN B) CORRESPONDING TO YOPD56-65 FROM YERSINIA ENTEROCOLITICA VIRULENCE PLASMID PYVE227 FROM STRAIN W22703.N-TERMINALLY ACETYLATED AND C-TERMINALLY AMIDATED

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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: 4.82 Å3/Da / Density % sol: 74.5 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: RESERVOIR SOLUTION: 50 MM MES PH 6, 50 MM CITRATE PH 5, 1.1-1.4 M (NH4)2SO4. VAPOR DIFFUSION AT 293 K WITH DROP RATIO OF 1 TO 0.5 PROTEIN TO RESERVOIR. PROTEIN CONCENTRATION 8 MG/ML. 1.3 ...Details: RESERVOIR SOLUTION: 50 MM MES PH 6, 50 MM CITRATE PH 5, 1.1-1.4 M (NH4)2SO4. VAPOR DIFFUSION AT 293 K WITH DROP RATIO OF 1 TO 0.5 PROTEIN TO RESERVOIR. PROTEIN CONCENTRATION 8 MG/ML. 1.3 FOLD MOLAR EXCESS OF PEPTIDE OVER PROTEIN.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2011 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 11931 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 69.59 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 10 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.1 / % possible all: 97

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Processing

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

2vgy


Resolution: 2.5→23.676 Å / SU ML: 0.85 / σ(F): 1.34 / Phase error: 21.84 / Stereochemistry target values: ML
Details: RESIDUES 21-28 AND 160-163 FROM CHAIN A ARE DISORDERED, RESIDUES 65 FROM CHAIN B IS DISORDERED
RfactorNum. reflection% reflection
Rfree0.2381 588 4.9 %
Rwork0.1899 --
obs0.1921 11901 99.32 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.501 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso mean: 79.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.2738 Å20 Å20 Å2
2--5.2738 Å20 Å2
3----10.5477 Å2
Refinement stepCycle: LAST / Resolution: 2.5→23.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 0 35 17 1168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071180
X-RAY DIFFRACTIONf_angle_d1.0611585
X-RAY DIFFRACTIONf_dihedral_angle_d16.576441
X-RAY DIFFRACTIONf_chiral_restr0.069176
X-RAY DIFFRACTIONf_plane_restr0.006201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.75150.34821640.31342751X-RAY DIFFRACTION98
2.7515-3.14890.27321330.21762805X-RAY DIFFRACTION100
3.1489-3.96420.20341450.17212845X-RAY DIFFRACTION100
3.9642-23.67690.23441460.17972912X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2046-1.5407-0.44122.74051.34380.95260.53750.0997-0.553-0.5779-0.3269-0.595-0.30990.2135-0.09290.4624-0.10760.12490.55390.18670.8502-37.58426.525613.9266
20.45640.009-0.3842.1747-0.33610.35160.3206-0.4733-0.09150.5288-0.3763-0.22290.0043-0.086500.6-0.033-0.09390.45230.10980.6452-44.62079.101619.3299
30.59360.1137-0.71292.27451.19471.5960.2166-0.7345-0.14230.3567-0.34810.4026-0.2058-0.45510.00040.6152-0.1332-0.00010.52310.01540.4375-51.952121.016923.2856
40.77760.05620.52020.89490.56990.6202-0.23820.83430.5467-0.8087-0.0595-0.1046-1.4513-0.127-0.10021.05530.0230.09690.8329-0.10760.5453-52.170432.942217.8576
51.7825-0.060.1070.6040.89521.31020.21650.35712.3842-1.1572-0.6712-0.7293-1.12720.08460.00010.7198-0.0197-0.09440.5053-0.01030.8931-41.018718.505111.7015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 29:56)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 57:86)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 87:133)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 134:159)
5X-RAY DIFFRACTION5CHAIN B

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