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- PDB-6rre: SidD, deAMPylase from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 6rre
TitleSidD, 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 / host cell perinuclear region of cytoplasm / hydrolase activity / metal ion binding
Similarity search - Function
Phosphatase 2c; domain 1 - #20 / : / : / SidD, catalytic domain / SidD, C-terminal / Phosphatase 2c; domain 1 / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Adenosine monophosphate-protein hydrolase SidD / SidD
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.586 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 17, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
E: Adenosine monophosphate-protein hydrolase SidD
F: Adenosine monophosphate-protein hydrolase SidD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,90610
Polymers317,8096
Non-polymers974
Water181
1
A: Adenosine monophosphate-protein hydrolase SidD


Theoretical massNumber of molelcules
Total (without water)52,9681
Polymers52,9681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenosine monophosphate-protein hydrolase SidD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9922
Polymers52,9681
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Adenosine monophosphate-protein hydrolase SidD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9922
Polymers52,9681
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Adenosine monophosphate-protein hydrolase SidD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9922
Polymers52,9681
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Adenosine monophosphate-protein hydrolase SidD


Theoretical massNumber of molelcules
Total (without water)52,9681
Polymers52,9681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Adenosine monophosphate-protein hydrolase SidD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9922
Polymers52,9681
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.570, 141.643, 234.298
Angle α, β, γ (deg.)90.000, 92.750, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11(chain A and (resid 40 through 72 or resid 89...
21(chain B and (resid 40 through 72 or resid 89...
31(chain C and (resid 40 through 72 or resid 89...
41(chain D and (resid 40 through 72 or resid 89...
51(chain E and (resid 40 through 72 or resid 89...
61(chain F and (resid 40 through 72 or resid 89...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILESERSER(chain A and (resid 40 through 72 or resid 89...AA40 - 724 - 36
12ASPASPVALVAL(chain A and (resid 40 through 72 or resid 89...AA89 - 26753 - 231
13ILEILELYSLYS(chain A and (resid 40 through 72 or resid 89...AA279 - 316243 - 280
14METMETASPASP(chain A and (resid 40 through 72 or resid 89...AA37 - 4951 - 459
21ILEILESERSER(chain B and (resid 40 through 72 or resid 89...BB40 - 724 - 36
22ASPASPVALVAL(chain B and (resid 40 through 72 or resid 89...BB89 - 26753 - 231
23ILEILELYSLYS(chain B and (resid 40 through 72 or resid 89...BB279 - 316243 - 280
24METMETALAALA(chain B and (resid 40 through 72 or resid 89...BB37 - 4941 - 458
25ASNASNILEILE(chain B and (resid 40 through 72 or resid 89...BB383 - 477347 - 441
26ASPASPALAALA(chain B and (resid 40 through 72 or resid 89...BB484 - 494448 - 458
31ILEILESERSER(chain C and (resid 40 through 72 or resid 89...CC40 - 724 - 36
32ASPASPVALVAL(chain C and (resid 40 through 72 or resid 89...CC89 - 26753 - 231
33ILEILELYSLYS(chain C and (resid 40 through 72 or resid 89...CC279 - 316243 - 280
34GLNGLNSERSER(chain C and (resid 40 through 72 or resid 89...CC322 - 359286 - 323
35ARGARGILEILE(chain C and (resid 40 through 72 or resid 89...CC38 - 4972 - 461
41ILEILESERSER(chain D and (resid 40 through 72 or resid 89...DD40 - 724 - 36
42ASPASPVALVAL(chain D and (resid 40 through 72 or resid 89...DD89 - 26753 - 231
43ILEILEILEILE(chain D and (resid 40 through 72 or resid 89...DD275239
44VALVALLYSLYS(chain D and (resid 40 through 72 or resid 89...DD280 - 316244 - 280
45GLNGLNSERSER(chain D and (resid 40 through 72 or resid 89...DD322 - 359286 - 323
46ASNASNILEILE(chain D and (resid 40 through 72 or resid 89...DD383 - 477347 - 441
47ASPASPALAALA(chain D and (resid 40 through 72 or resid 89...DD484 - 494448 - 458
51ILEILESERSER(chain E and (resid 40 through 72 or resid 89...EE40 - 724 - 36
52ASPASPVALVAL(chain E and (resid 40 through 72 or resid 89...EE89 - 26753 - 231
53ILEILELYSLYS(chain E and (resid 40 through 72 or resid 89...EE279 - 316243 - 280
54GLNGLNILEILE(chain E and (resid 40 through 72 or resid 89...EE322 - 477286 - 441
55ASPASPALAALA(chain E and (resid 40 through 72 or resid 89...EE484 - 494448 - 458
61ILEILESERSER(chain F and (resid 40 through 72 or resid 89...FF40 - 724 - 36
62ASPASPVALVAL(chain F and (resid 40 through 72 or resid 89...FF89 - 26753 - 231
63ILEILESERSER(chain F and (resid 40 through 72 or resid 89...FF279 - 359243 - 323
64ASNASNILEILE(chain F and (resid 40 through 72 or resid 89...FF383 - 477347 - 441
65ASPASPALAALA(chain F and (resid 40 through 72 or resid 89...FF484 - 494448 - 458

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Components

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


Mass: 52968.137 Da / Num. of mol.: 6
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
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.32 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.88 Sodium Formate, 0.09M Tris pH 8 0.1% Anapoe 35

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99996 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 3.59→46.806 Å / Num. obs: 48162 / % possible obs: 98.8 % / Redundancy: 3.385 % / Biso Wilson estimate: 135.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rrim(I) all: 0.151 / Χ2: 1.124 / Net I/σ(I): 6.1 / Num. measured all: 163031
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
3.59-3.83.4151.2220.9125465780474570.611.44395.6
3.8-4.063.4460.7581.5625222733473190.8110.89899.8
4.06-4.393.2950.422.722455683368140.9130.50399.7
4.39-4.83.5160.2085.2922094633062830.9810.24599.3
4.8-5.363.4350.1766.0819618573657120.9860.20999.6
5.36-6.183.3740.1666.5417019505750440.9840.19899.7
6.18-7.533.470.1089.6414815428442690.9940.12899.6
7.53-10.523.1640.0420.6610617339933560.9980.04898.7
10.52-46.8063.0010.03724.045726198819080.9980.04596

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.586→46.806 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 42.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3377 2431 5.07 %
Rwork0.2952 45481 -
obs0.2975 47912 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 215.07 Å2 / Biso mean: 136.1728 Å2 / Biso min: 53.69 Å2
Refinement stepCycle: final / Resolution: 3.586→46.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19773 0 4 1 19778
Biso mean--117.84 107.06 -
Num. residues----2497
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7053X-RAY DIFFRACTION8.593TORSIONAL
12B7053X-RAY DIFFRACTION8.593TORSIONAL
13C7053X-RAY DIFFRACTION8.593TORSIONAL
14D7053X-RAY DIFFRACTION8.593TORSIONAL
15E7053X-RAY DIFFRACTION8.593TORSIONAL
16F7053X-RAY DIFFRACTION8.593TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5862-3.65940.46931090.43912383249288
3.6594-3.73890.4181440.38062759290399
3.7389-3.82590.45661630.381826152778100
3.8259-3.92150.39611490.371726932842100
3.9215-4.02750.42571420.35462688283099
4.0275-4.14590.43121710.34892659283099
4.1459-4.27960.4221480.34772713286199
4.2796-4.43250.34461180.29592717283599
4.4325-4.60980.34161180.2722679279799
4.6098-4.81940.3361430.27432694283799
4.8194-5.07320.32061520.27992678283099
5.0732-5.39060.33891350.27292722285799
5.3906-5.80610.35551310.290127542885100
5.8061-6.38910.34411540.316126942848100
6.3891-7.31060.36531490.31082698284799
7.3106-9.19910.28611470.25612721286898
9.1991-46.80970.26951580.25672614277295

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