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- PDB-2bho: Crystal structure of the Yersinia enterocolitica type III secreti... -

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Basic information

Entry
Database: PDB / ID: 2bho
TitleCrystal structure of the Yersinia enterocolitica type III secretion chaperone SycT
ComponentsCHAPERONE PROTEIN SYCT
KeywordsCHAPERONE / YERSINIA / SECRETION
Function / homology
Function and homology information


protein secretion by the type III secretion system
Similarity search - Function
Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chaperone protein SycT / Chaperone protein SycT
Similarity search - Component
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsGroll, M. / Wilharm, G.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of the Yersinia Enterocolitica Type III Secretion Chaperone Syct
Authors: Locher, M. / Lehnert, B. / Krauss, K. / Heesemann, J. / Groll, M. / Wilharm, G.
History
DepositionJan 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHAPERONE PROTEIN SYCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3752
Polymers15,1801
Non-polymers1951
Water39622
1
A: CHAPERONE PROTEIN SYCT
hetero molecules

A: CHAPERONE PROTEIN SYCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7504
Polymers30,3602
Non-polymers3902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)91.170, 45.834, 34.453
Angle α, β, γ (deg.)90.00, 105.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2015-

HOH

21A-2016-

HOH

31A-2017-

HOH

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Components

#1: Protein CHAPERONE PROTEIN SYCT


Mass: 15180.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Plasmid: PMS470 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O85243, UniProt: P0C2V9*PLUS
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIT IS AS A SPECIFIC CHAPERONE FOR YOPT
Sequence detailsVARIANT S -> P (IN PLASMID PYVE8081 AND PLASMID PYVA127/90).

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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: 1.34 Å3/Da / Density % sol: 46 %
Crystal growpH: 7
Details: 1.2 M DL-MALIC ACID, PH 7.0 100MM BIS-TRIS PROPANE, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.0723, 1.0719, 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 14, 2004 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07231
21.07191
30.981
ReflectionResolution: 2.5→99 Å / Num. obs: 99007 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 36.5
Reflection shellResolution: 2.51→2.54 Å / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 6 / % possible all: 88.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.914 / SU B: 32.085 / SU ML: 0.298 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 2.546 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.259 432 10.2 %RANDOM
Rwork0.244 ---
obs0.245 3790 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: 44.45 Å2
Baniso -1Baniso -2Baniso -3
1--5.01 Å20 Å2-1.23 Å2
2--10.16 Å20 Å2
3----5.79 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 1 22 932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021932
X-RAY DIFFRACTIONr_bond_other_d00.02807
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.921267
X-RAY DIFFRACTIONr_angle_other_deg3.59231881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.175109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.89725.74154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.05215156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.771153
X-RAY DIFFRACTIONr_chiral_restr0.0960.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021045
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02186
X-RAY DIFFRACTIONr_nbd_refined0.2740.2249
X-RAY DIFFRACTIONr_nbd_other0.310.2863
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2451
X-RAY DIFFRACTIONr_nbtor_other0.120.2457
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3450.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0350.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5051.5714
X-RAY DIFFRACTIONr_mcbond_other0.4721.5226
X-RAY DIFFRACTIONr_mcangle_it3.0482879
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6743458
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.4134.5388
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: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 28 -
Rwork0.308 278 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 4.4751 Å / Origin y: -3.2598 Å / Origin z: 24.0678 Å
111213212223313233
T0.1023 Å20.0145 Å2-0.0564 Å2-0.2339 Å2-0.0709 Å2--0.1428 Å2
L9.3639 °20.3748 °20.3366 °2-6.1189 °2-1.1418 °2--10.9208 °2
S0.0302 Å °-1.0058 Å °0.044 Å °0.5266 Å °-0.0325 Å °-0.3539 Å °-0.2512 Å °1.2821 Å °0.0023 Å °

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