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- PDB-4g2b: Structure of the Catalytic Domain of the Salmonella Virulence Fac... -

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Basic information

Entry
Database: PDB / ID: 4g2b
TitleStructure of the Catalytic Domain of the Salmonella Virulence Factor SseI
ComponentsSecreted effector protein sseI
KeywordsPROTEIN BINDING / cysteine protease superfamily
Function / homologyTox-PLDMTX domain / Dermonecrotoxin of the Papain-like fold / Secreted effector protein ssei fold / Secreted effector protein ssei. / host cell cytoplasm / Roll / extracellular region / Alpha Beta / Secreted effector protein SseI
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsStebbins, C.E. / Bhaskaran, S.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of the catalytic domain of the Salmonella virulence factor SseI.
Authors: Bhaskaran, S.S. / Stebbins, C.E.
History
DepositionJul 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Secreted effector protein sseI
B: Secreted effector protein sseI


Theoretical massNumber of molelcules
Total (without water)42,6542
Polymers42,6542
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-9 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.818, 62.506, 110.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Secreted effector protein sseI


Mass: 21327.148 Da / Num. of mol.: 2 / Fragment: UNP residues 137-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: sseI, srfH, STM1051 / References: UniProt: Q8ZQ79
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Crystallization screens were conducted using 1:1 sitting drops at RT and 4 C. The C-terminal domain (137-322) (~20mg/mL) gave large rectangular crystals in 1.15M LiSO4, 0.1M NaOAc, pH 4.6 (4 ...Details: Crystallization screens were conducted using 1:1 sitting drops at RT and 4 C. The C-terminal domain (137-322) (~20mg/mL) gave large rectangular crystals in 1.15M LiSO4, 0.1M NaOAc, pH 4.6 (4 C) when optimized (1:1 hanging drops). However these were very fragile and consisted of multiple lattices overlaid on each other as observed in their diffraction patterns. SseI 137-322 was then reductively methylated and rescreened. It gave multiple crystals of differing morphologies in a number of conditions containing MES, Tris, and HEPES buffers pH 6.0 - 9.0, and 1.6 to 2.0M (NH4)SO4. To obtain single crystals, crystals from 0.1M MES pH 7.1, 1.8M (NH4)SO4 were crushed and microseeded into pre-equilibrated (2 hrs) drops containing protein/reservoir solution (0.1M MES pH 5.5, 1.6M (NH4)SO4). This procedure produced single, small, rectangular crystals. To obtain larger crystals, single crystals obtained in the previous step were macroseeded into pre-equilibrated drops, giving large, thin rectangular plates that were well-diffracting. SeMet-substituted crystals of 137-322 were obtained in the same conditions but gave large crystals directly without any seeding. Crystals were then cryoprotected by transfer in small increments into mother liquor supplemented with 25% glycerol. , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionHighest resolution: 2.05 Å / Num. obs: 22722

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→27.18 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.493 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 1227 5.1 %RANDOM
Rwork0.19353 ---
obs0.19579 22722 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.336 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.05→27.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 0 158 2877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222785
X-RAY DIFFRACTIONr_bond_other_d0.0020.021904
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.943769
X-RAY DIFFRACTIONr_angle_other_deg0.9983.0014620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3575334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11724.468141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37415474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0631516
X-RAY DIFFRACTIONr_chiral_restr0.1220.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213102
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02584
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_it1.1891.51682
X-RAY DIFFRACTIONr_mcbond_other0.3271.5672
X-RAY DIFFRACTIONr_mcangle_it2.05722721
X-RAY DIFFRACTIONr_scbond_it3.22231103
X-RAY DIFFRACTIONr_scangle_it4.9754.51048
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 84 -
Rwork0.222 1619 -
obs--98.61 %

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