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- PDB-6p82: Structure of P. aeruginosa ATCC27853 CdnD, Apo form 1 -

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Basic information

Entry
Database: PDB / ID: 6p82
TitleStructure of P. aeruginosa ATCC27853 CdnD, Apo form 1
ComponentsNucleotidyltransferase
KeywordsSIGNALING PROTEIN / second-messenger signaling / cGAS / CD-NTase
Function / homology
Function and homology information


diadenylate cyclase / diadenylate cyclase activity / nucleotide metabolic process / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / ATP binding / metal ion binding
Similarity search - Function
: / Second Messenger Oligonucleotide or Dinucleotide Synthetase domain / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CBASS oligonucleotide cyclase / Cyclic AMP-AMP-AMP synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsYe, Q. / Corbett, K.D.
CitationJournal: Mol.Cell / Year: 2020
Title: HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-like Enzymes to Mediate Bacteriophage Immunity.
Authors: Ye, Q. / Lau, R.K. / Mathews, I.T. / Birkholz, E.A. / Watrous, J.D. / Azimi, C.S. / Pogliano, J. / Jain, M. / Corbett, K.D.
History
DepositionJun 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleotidyltransferase
B: Nucleotidyltransferase
C: Nucleotidyltransferase
D: Nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,64638
Polymers137,3804
Non-polymers3,26634
Water11,151619
1
A: Nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,30611
Polymers34,3451
Non-polymers96110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1149
Polymers34,3451
Non-polymers7698
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1149
Polymers34,3451
Non-polymers7698
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1149
Polymers34,3451
Non-polymers7698
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.589, 117.387, 147.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11D-405-

SO4

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Components

#1: Protein
Nucleotidyltransferase / Nucleotidyltransferase domain protein


Mass: 34345.074 Da / Num. of mol.: 4 / Mutation: N-terminal SNA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: DY979_07585, EGY23_20895, IPC669_24880, PA5486_02902, PAERUG_E15_London_28_01_14_04351, PAMH19_6112
Production host: Escherichia coli (E. coli) / References: UniProt: A0A080VY32, UniProt: P0DTF7*PLUS
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 62.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5 and 1.8-2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→147.8 Å / Num. obs: 113653 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.058 / Rrim(I) all: 0.15 / Net I/σ(I): 10.5
Reflection shellResolution: 2.05→2.08 Å / Redundancy: 5.3 % / Rmerge(I) obs: 2.033 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5059 / CC1/2: 0.336 / Rpim(I) all: 0.906 / Rrim(I) all: 2.234 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→91.923 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 26.15
RfactorNum. reflection% reflection
Rfree0.2426 5703 5.01 %
Rwork0.2127 --
obs0.2142 113614 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→91.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9648 0 170 619 10437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710016
X-RAY DIFFRACTIONf_angle_d0.82513557
X-RAY DIFFRACTIONf_dihedral_angle_d14.2415923
X-RAY DIFFRACTIONf_chiral_restr0.0471389
X-RAY DIFFRACTIONf_plane_restr0.0051764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07050.41442550.36784497X-RAY DIFFRACTION64
2.0705-2.09490.33633810.3376957X-RAY DIFFRACTION99
2.0949-2.12040.33473770.3236904X-RAY DIFFRACTION99
2.1204-2.14730.34493380.30947038X-RAY DIFFRACTION100
2.1473-2.17550.31694050.30216968X-RAY DIFFRACTION100
2.1755-2.20530.29433880.29846930X-RAY DIFFRACTION100
2.2053-2.23690.32093610.29427021X-RAY DIFFRACTION100
2.2369-2.27020.32793940.30656871X-RAY DIFFRACTION98
2.2702-2.30570.3074290.28416900X-RAY DIFFRACTION99
2.3057-2.34350.29913780.2826954X-RAY DIFFRACTION99
2.3435-2.38390.29463270.27727002X-RAY DIFFRACTION100
2.3839-2.42730.30894240.27716986X-RAY DIFFRACTION100
2.4273-2.4740.31933320.26326952X-RAY DIFFRACTION99
2.474-2.52450.2823710.26336960X-RAY DIFFRACTION99
2.5245-2.57940.31583860.24386995X-RAY DIFFRACTION100
2.5794-2.63940.25253930.23416923X-RAY DIFFRACTION99
2.6394-2.70540.27333310.23786978X-RAY DIFFRACTION99
2.7054-2.77860.29663400.23126980X-RAY DIFFRACTION99
2.7786-2.86030.2853730.23226984X-RAY DIFFRACTION99
2.8603-2.95260.25943550.22256995X-RAY DIFFRACTION100
2.9526-3.05820.2583510.21757010X-RAY DIFFRACTION100
3.0582-3.18060.25033760.2096979X-RAY DIFFRACTION100
3.1806-3.32540.25013650.20336969X-RAY DIFFRACTION100
3.3254-3.50070.22993660.19266971X-RAY DIFFRACTION99
3.5007-3.72010.20923200.18916954X-RAY DIFFRACTION99
3.7201-4.00730.19323660.16816956X-RAY DIFFRACTION99
4.0073-4.41060.18593510.16116998X-RAY DIFFRACTION99
4.4106-5.04870.18973530.1676967X-RAY DIFFRACTION99
5.0487-6.36070.22093470.19466968X-RAY DIFFRACTION99
6.3607-92.01580.1893680.18116916X-RAY DIFFRACTION98

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