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- PDB-5kdg: Crystal Structure of Salmonella Typhimurium Effector GtgE -

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Basic information

Entry
Database: PDB / ID: 5kdg
TitleCrystal Structure of Salmonella Typhimurium Effector GtgE
ComponentsGifsy-2 prophage protein
KeywordsHYDROLASE / papain-like fold / cysteine protease / virulence factor / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / PSI-Biology
Function / homology: / GtgE peptidase / Gifsy-2 prophage protein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsKozlov, G. / Xu, C. / Wong, K. / Gehring, K. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)GSP-48370 Canada
CitationJournal: PLoS ONE / Year: 2016
Title: Crystal Structure of the Salmonella Typhimurium Effector GtgE.
Authors: Xu, C. / Kozlov, G. / Wong, K. / Gehring, K. / Cygler, M.
History
DepositionJun 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gifsy-2 prophage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3666
Polymers22,8891
Non-polymers4765
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Gifsy-2 prophage protein
hetero molecules

A: Gifsy-2 prophage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,73212
Polymers45,7792
Non-polymers95310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7150 Å2
ΔGint-142 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.302, 64.302, 124.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsMonomer as determined by size-exclusion chromatography

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Components

#1: Protein Gifsy-2 prophage protein / Uncharacterized protein / Virulence protein


Mass: 22889.432 Da / Num. of mol.: 1 / Fragment: residues 17-217 / Mutation: C45S, D123N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: SBOV09681, DD95_21385, ERS450001_01848, SEETMRM9437_5135, TJ44_09000
Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9XC73, papain
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.8 M ammonium sulfate, 0.1 M Bis-Tris (pH 5.5) and 20% (w/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6362 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6362 Å / Relative weight: 1
ReflectionResolution: 1.73→57.1 Å / Num. obs: 26504 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rsym value: 0.042 / Net I/σ(I): 37.8
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mi7

4mi7


Resolution: 1.73→57.1 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.137 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.23813 1343 4.8 %RANDOM
Rwork0.20909 ---
obs0.21051 26504 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.084 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.73→57.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 26 64 1589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191562
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0091.9542118
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211184
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9142.043746
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.543.053930
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.382.281816
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.01521.4361885
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: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 99 -
Rwork0.259 1912 -
obs--99.95 %
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)
14.17722.919-2.35174.01140.948512.58130.0616-0.7525-0.11460.555-0.2057-0.49860.61140.79280.14420.16690.1211-0.06370.26070.02180.2157-19.084-17.785821.0475
22.33520.10160.77492.91471.84068.00270.03330.0191-0.136-0.1771-0.13550.37570.2682-0.68920.10230.0937-0.00340.00710.0766-0.01840.1554-21.6971-27.2422-9.9654
35.0447-2.2556-2.56284.9695-0.34925.1219-0.17460.2957-0.57730.3543-0.10550.52010.2709-0.05370.28010.1608-0.04280.07320.0494-0.04150.1158-23.7175-31.30260.829
44.13233.14472.88476.11972.8898.3976-0.0284-0.3178-0.1060.3059-0.0653-0.27970.47620.25740.09370.17810.02130.02810.0736-0.00860.1147-15.6407-37.6373-7.9041
51.65170.2058-0.1041.36010.29942.5692-0.0532-0.0066-0.0093-0.14470.0577-0.1531-0.0360.3975-0.00450.10080.010.01850.0973-0.01270.0979-4.2168-21.5406-14.1351
612.04827.51710.893516.876319.718723.5552-0.07-0.54580.09190.5309-0.14230.21950.5504-0.28660.21230.11720.0092-0.04920.29670.05830.5422-1.6776-32.09950.9185
74.10130.76872.07092.93870.83317.404-0.007-0.0185-0.2043-0.09870.0274-0.01810.4275-0.0269-0.02040.1540.02070.03090.0248-0.02460.1091-12.1219-32.4887-16.6736
81.90563.1465-2.974416.1485-20.623328.7150.21150.05150.59810.38340.49941.0199-1.3569-0.946-0.71090.66380.1927-0.07590.081-0.02080.3092-17.483-22.9159-39.5607
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 31
2X-RAY DIFFRACTION2A32 - 64
3X-RAY DIFFRACTION3A65 - 83
4X-RAY DIFFRACTION4A84 - 96
5X-RAY DIFFRACTION5A97 - 195
6X-RAY DIFFRACTION6A196 - 200
7X-RAY DIFFRACTION7A201 - 213
8X-RAY DIFFRACTION8A214 - 220

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