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- PDB-4ksn: C-terminal domain of SdbC protein from Legionella pneumophila. -

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Basic information

Entry
Database: PDB / ID: 4ksn
TitleC-terminal domain of SdbC protein from Legionella pneumophila.
ComponentsSdbC
KeywordsStructural Genomics / Unknown Function / APC105586 / SdbC / effector protein / unknown ligand / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologyDouble Stranded RNA Binding Domain - #80 / Double Stranded RNA Binding Domain / Other non-globular / Special / Alpha/Beta hydrolase fold / Unknown ligand / SdbC
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsOsipiuk, J. / Evdokimova, E. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: C-terminal domain of SdbC protein from Legionella pneumophila.
Authors: Osipiuk, J. / Evdokimova, E. / Savchenko, A. / Joachimiak, A.
History
DepositionMay 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SdbC
B: SdbC
C: SdbC
D: SdbC


Theoretical massNumber of molelcules
Total (without water)35,24723
Polymers35,2474
Non-polymers019
Water3,027168
1
A: SdbC
B: SdbC
C: SdbC
D: SdbC

A: SdbC
B: SdbC
C: SdbC
D: SdbC


Theoretical massNumber of molelcules
Total (without water)70,49446
Polymers70,4948
Non-polymers038
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area20070 Å2
ΔGint-141 kcal/mol
Surface area25520 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-60 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.240, 57.928, 81.448
Angle α, β, γ (deg.)90.00, 121.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
SdbC


Mass: 8811.710 Da / Num. of mol.: 4 / Mutation: L382M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / Gene: lpg2391, sdbC / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZSX5
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 19 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30% Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.86→45.77 Å / Num. all: 29977 / Num. obs: 29977 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.87-1.93.80.6291.99194.5
1.9-1.944.40.536198.7
1.94-1.974.90.4371100
1.97-2.015.50.3741100
2.01-2.065.80.321100
2.06-2.115.80.2621100
2.11-2.165.80.2261100
2.16-2.225.80.2021100
2.22-2.285.80.171100
2.28-2.365.80.1521100
2.36-2.445.80.1371100
2.44-2.545.80.1251100
2.54-2.655.80.1071100
2.65-2.795.80.0871100
2.79-2.975.80.0741100
2.97-3.25.80.062199.9
3.2-3.525.60.0541100
3.52-4.035.60.051199.9
4.03-5.075.50.043199.9
5.07-505.50.047198

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→45.77 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.745 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22488 1525 5.1 %RANDOM
Rwork0.18778 ---
obs0.18975 28452 99.36 %-
all-29977 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.259 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å21.59 Å2
2---2.19 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.86→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 19 168 2135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192033
X-RAY DIFFRACTIONr_bond_other_d0.0010.021972
X-RAY DIFFRACTIONr_angle_refined_deg1.7472.0222772
X-RAY DIFFRACTIONr_angle_other_deg0.78534575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9985252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01624.65988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05515356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.312159
X-RAY DIFFRACTIONr_chiral_restr0.0990.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02411
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 98 -
Rwork0.269 1960 -
obs--93 %
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)
12.41450.6002-2.64990.7131-0.33173.1191-0.13240.22610.0324-0.10730.09320.19850.1031-0.26990.03910.05220.0283-0.06620.22030.0330.140636.203135.256542.5834
22.1131-0.02760.37571.118-0.73860.7256-0.0407-0.02220.0808-0.14750.0655-0.23530.1802-0.0419-0.02480.06630.0108-0.06160.1447-0.01350.246346.153624.949238.0921
32.060.74641.09582.61580.50112.9008-0.00790.37770.0822-0.17490.0039-0.4415-0.23450.2940.0040.12050.004-0.02390.25050.01060.143940.429934.179615.9163
41.3921-0.38770.86810.3384-0.17210.56450.0696-0.0288-0.25280.05470.08890.04810.0662-0.0139-0.15850.033-0.0063-0.01780.213-0.02230.052135.697221.642821.4195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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