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- PDB-4g29: Structure of the Catalytic Domain of the Salmonella Virulence Fac... -

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Basic information

Entry
Database: PDB / ID: 4g29
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 / SAD / Resolution: 1.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Secreted effector protein sseI


Theoretical massNumber of molelcules
Total (without water)21,6551
Polymers21,6551
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.256, 52.256, 132.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Secreted effector protein sseI


Mass: 21655.412 Da / Num. of mol.: 1 / 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.: 137 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 277.15 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 277.15K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionHighest resolution: 1.7 Å / Num. obs: 19151

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→19.08 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.345 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21364 1045 5.2 %RANDOM
Rwork0.18318 ---
obs0.18469 19151 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.984 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 0 137 1472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221367
X-RAY DIFFRACTIONr_bond_other_d0.0060.02925
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.941850
X-RAY DIFFRACTIONr_angle_other_deg0.99832252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1835164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04424.92869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55715231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.858156
X-RAY DIFFRACTIONr_chiral_restr0.1050.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02281
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_it1.0111.5828
X-RAY DIFFRACTIONr_mcbond_other0.3391.5331
X-RAY DIFFRACTIONr_mcangle_it1.70521338
X-RAY DIFFRACTIONr_scbond_it2.9823539
X-RAY DIFFRACTIONr_scangle_it4.2224.5512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.702→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 70 -
Rwork0.297 1185 -
obs--100 %
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)
16.1234-2.724-1.45069.3188-2.56657.20730.25290.21470.4038-0.0998-0.1312-0.7355-0.38750.8526-0.12160.0701-0.09970.03440.2296-0.02280.115334.29816.63214.992
23.94380.0328-2.13651.0664-0.61263.57950.1287-0.28550.32930.26060.0606-0.0548-0.46320.39-0.18930.1353-0.0220.03380.0956-0.02740.090923.18416.824.888
33.741-5.29241.93197.4915-2.76152.76680.1416-0.0691-0.2726-0.22330.05870.39090.20230.0757-0.20040.12910.0042-0.01150.12560.01680.100121.4744.95425.764
42.35280.2407-0.58770.2130.11462.79950.1127-0.01180.2525-0.0396-0.01490.1112-0.2920.0343-0.09790.14210.00850.0230.08510.00760.133317.41115.80613.571
52.04790.2595-0.14362.71140.36391.4324-0.0389-0.004-0.21160.027-0.0121-0.11140.15750.02460.05090.1322-0.00120.03120.11160.01690.095821.722-3.2438.888
62.9599-0.49170.45392.58260.49683.3909-0.02850.07240.21790.01410.0851-0.0944-0.22120.2743-0.05660.1139-0.02370.02770.1472-0.00370.123126.45911.94312.518
71.9944-0.8611.36793.6480.79073.60160.0614-0.09-0.1750.13420.17-0.17390.26960.4179-0.23140.08740.00150.0080.1728-0.0140.110331.8445.42713.494
87.9389-0.57074.55994.677-0.465212.9543-0.0487-0.27520.18860.299-0.0486-0.4912-0.33620.55090.09740.12690.04010.04110.19810.00040.169533.559-1.3957.529
91.57070.9655-0.39911.22240.08211.209-0.13260.2296-0.1241-0.13490.07290.07560.0895-0.12050.05980.1117-0.00890.01650.11130.00270.087118.522-1.5073.172
107.91210.95110.973411.55332.394110.0223-0.01740.374-0.3119-0.45410.2101-0.30860.21850.2438-0.19280.09510.02510.02640.0727-0.01740.129231.206-11.233-2.454
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A145 - 154
2X-RAY DIFFRACTION2A155 - 167
3X-RAY DIFFRACTION3A168 - 177
4X-RAY DIFFRACTION4A178 - 198
5X-RAY DIFFRACTION5A199 - 220
6X-RAY DIFFRACTION6A221 - 238
7X-RAY DIFFRACTION7A239 - 260
8X-RAY DIFFRACTION8A261 - 268
9X-RAY DIFFRACTION9A269 - 304
10X-RAY DIFFRACTION10A305 - 313

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