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- PDB-4o2i: The crystal structure of non-LEE encoded type III effector C from... -

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Basic information

Entry
Database: PDB / ID: 4o2i
TitleThe crystal structure of non-LEE encoded type III effector C from Citrobacter rodentium
ComponentsNon-LEE encoded type III effector C
KeywordsHYDROLASE / type 3 effector / PSI-biology / Midwest Center for Structural Genomics / MCSG / Program for the Characterization of Secreted Effector Proteins / PCSEP
Function / homologyNFkB-p65-degrading zinc protease / NFkB-p65-degrading zinc protease / metal ion binding / Non-LEE encoded type III effector C
Function and homology information
Biological speciesCitrobacter rodentium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsChang, C. / Xu, X. / Cui, H. / Savchenko, A. / Adkins, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP)
CitationJournal: To be Published
Title: The crystal structure of non-LEE encoded type III effector C from Citrobacter rodentium
Authors: Chang, C. / Xu, X. / Cui, H. / Savchenko, A. / Adkins, J. / Joachimiak, A.
History
DepositionDec 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-LEE encoded type III effector C
B: Non-LEE encoded type III effector C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5384
Polymers73,4072
Non-polymers1312
Water2,378132
1
A: Non-LEE encoded type III effector C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7692
Polymers36,7041
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-LEE encoded type III effector C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7692
Polymers36,7041
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.937, 89.356, 205.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Non-LEE encoded type III effector C


Mass: 36703.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter rodentium (bacteria) / Gene: nleC / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RYA8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.1 M Sodium Cacodylate, 0.2 M Calcium acetate, 19% PEG8000, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 22, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.2→102.71 Å / Num. all: 35042 / Num. obs: 33150 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Rmerge(I) obs: 0.099 / Χ2: 1.99 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.2-2.2211.87391.328183.9
2.22-2.2412.17481.066185.30.945
2.24-2.2612.57180.953189.10.675
2.26-2.2812.87351.318185.7
2.28-2.312.67661.239186.9
2.3-2.32137521.113187.90.881
2.32-2.3513.37581.1011880.817
2.35-2.3713.47341.053187.90.751
2.37-2.413.27951.069189.60.694
2.4-2.4213.17901.032191.80.684
2.42-2.4513.47621.039190.20.619
2.45-2.4813.37951.009190.50.528
2.48-2.5112.88191.0331960.457
2.51-2.5413.28181.032193.10.445
2.54-2.5713.27841195.30.396
2.57-2.6112.78651.011197.20.354
2.61-2.6513.27990.991930.298
2.65-2.69138311.043198.50.291
2.69-2.7312.98471.057196.70.277
2.73-2.77138601.116198.50.253
2.77-2.8213.28251.13197.60.21
2.82-2.8713.18581.203197.30.184
2.87-2.9313.18561.265199.80.172
2.93-2.9913.48381.282197.30.159
2.99-3.0513.18881.384199.60.138
3.05-3.1213.58191.419197.60.133
3.12-3.213.18891.597199.10.119
3.2-3.2913.68461.783199.40.108
3.29-3.3813.68742.013198.40.1
3.38-3.4913.68522.2911000.099
3.49-3.6213.78862.464198.90.089
3.62-3.7613.78442.794198.80.083
3.76-3.9313.88833.076199.40.075
3.93-4.1413.68903.273199.10.072
4.14-4.413.88613.546199.70.072
4.4-4.7413.78903.829199.60.069
4.74-5.2113.69003.691199.80.065
5.21-5.9713.98824.456199.50.071
5.97-7.5214.19165.135199.50.066
7.52-5012.79386.942196.60.059

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
ARP/wARPmodel building
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.2→102.71 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.418 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.195
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 1656 5 %RANDOM
Rwork0.1679 ---
all0.1715 32927 --
obs0.1715 32927 94.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 167.37 Å2 / Biso mean: 71.4524 Å2 / Biso min: 27.86 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å20 Å2
2--2.18 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→102.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3921 0 2 132 4055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.024009
X-RAY DIFFRACTIONr_angle_refined_deg0.9631.955447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7215494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29724.312218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30615637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0341534
X-RAY DIFFRACTIONr_chiral_restr0.070.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213166
X-RAY DIFFRACTIONr_rigid_bond_restr1.46634009
X-RAY DIFFRACTIONr_sphericity_free46.917574
X-RAY DIFFRACTIONr_sphericity_bonded52.48853990
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 92 -
Rwork0.239 1893 -
all-1985 -
obs--82.02 %
Refinement TLS params.Method: refined / Origin x: -1.1819 Å / Origin y: 23.3783 Å / Origin z: 87.7245 Å
111213212223313233
T0.0055 Å20.0111 Å2-0.0004 Å2-0.077 Å2-0.0027 Å2--0.0652 Å2
L0.2723 °2-0.1539 °2-0.2259 °2-0.1009 °20.1765 °2--0.3798 °2
S0.0303 Å °0.0207 Å °0.012 Å °-0.0225 Å °-0.0277 Å °-0.0067 Å °-0.0413 Å °-0.0366 Å °-0.0026 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 52
2X-RAY DIFFRACTION1A53 - 170
3X-RAY DIFFRACTION1A171 - 279

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