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- PDB-6rp4: CDT of SidD, deAMPylase from Legionella pneumophila -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6rp4
TitleCDT of SidD, deAMPylase from Legionella pneumophila
ComponentsAdenosine monophosphate-protein hydrolase SidD
KeywordsHYDROLASE / Legionella pneumphila effector
Function / homology
Function and homology information


protein deadenylylation / protein adenylylhydrolase activity / protein adenylylation / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / regulation of GTPase activity / small GTPase binding / hydrolase activity / host cell perinuclear region of cytoplasm / metal ion binding
Similarity search - Function
: / : / SidD, catalytic domain / SidD, C-terminal
Similarity search - Domain/homology
Adenosine monophosphate-protein hydrolase SidD / SidD
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5 Å
AuthorsTascon, I. / Lucas, M. / Rojas, A.L. / Hierro, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2017-88766-R Spain
CitationJournal: Plos Pathog. / Year: 2020
Title: Structural insight into the membrane targeting domain of the Legionella deAMPylase SidD.
Authors: Tascon, I. / Li, X. / Lucas, M. / Nelson, D. / Vidaurrazaga, A. / Lin, Y.H. / Rojas, A.L. / Hierro, A. / Machner, M.P.
History
DepositionMay 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosine monophosphate-protein hydrolase SidD
B: Adenosine monophosphate-protein hydrolase SidD
C: Adenosine monophosphate-protein hydrolase SidD
D: Adenosine monophosphate-protein hydrolase SidD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,18919
Polymers70,3934
Non-polymers79615
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-222 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.579, 165.579, 68.712
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Adenosine monophosphate-protein hydrolase SidD / SidD


Mass: 17598.170 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_12395 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RCR2, UniProt: Q5ZSQ2*PLUS

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Non-polymers , 5 types, 73 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.88 Å3/Da / Density % sol: 68.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0M NaCl, 0.1M sodium acetate (pH 4.6) and 20% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9334 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.5
ReflectionResolution: 2.49→47.799 Å / Num. obs: 37987 / % possible obs: 99.8 % / Redundancy: 11.38 % / CC1/2: 1 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.101 / Χ2: 1.076 / Net I/σ(I): 21.76 / Num. measured all: 432311
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.49-2.6411.3591.9121.5169037611260780.5852.00199.4
2.64-2.8211.5281.1182.765733571257020.8231.1799.8
2.82-3.0411.5040.5046.2561535535553490.9630.52899.9
3.04-3.3311.5070.22413.1156524492249120.9920.23499.8
3.33-3.7211.490.10524.7851347446944690.9980.11100
3.72-4.311.4470.05640.0845480397439730.9990.058100
4.3-5.2511.3410.03854.89379253344334410.039100
5.25-7.3810.9890.04451.5429001263926390.9990.046100
7.38-47.79910.3410.02575.47157291535152110.02699.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.5→47.799 Å / Cross valid method: THROUGHOUT / σ(F): 50.12 / Phase error: 32.52 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2961 1936 5.18 %
Rwork0.2632 35390 -
obs0.2717 37398 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.19 Å2 / Biso mean: 65.5299 Å2 / Biso min: 17.81 Å2
Refinement stepCycle: final / Resolution: 2.5→47.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4002 0 35 58 4095
Biso mean--61.63 55.92 -
Num. residues----504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5007-2.56310.40581250.35582564268995
2.5631-2.63230.38791380.35782479261794
2.6323-2.70960.36831220.35132502262495
2.7096-2.79690.4181380.34022522266095
2.7969-2.89670.3991380.33282510264895
2.8967-3.01240.3321250.32552510263595
3.0124-3.14910.35551470.31832522266994
3.1491-3.31460.35431630.30462507267094
3.3146-3.52150.31051380.28152499263795
3.5215-3.79210.28341260.27772538266495
3.7921-4.17140.27791430.26032533267695
4.1714-4.76970.2551450.22832538268395
4.7697-5.98920.30011460.24842556270295
5.9892-22.01730.27411420.22292610275295

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