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- PDB-6p8u: Structure of P. aeruginosa ATCC27853 CdnD:HORMA2:Peptide 1 complex -

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Basic information

Entry
Database: PDB / ID: 6p8u
TitleStructure of P. aeruginosa ATCC27853 CdnD:HORMA2:Peptide 1 complex
Components
  • HORMA domain containing protein
  • Nucleotidyltransferase
  • Peptide 1
KeywordsSIGNALING PROTEIN / second-messenger signaling / cGAS / CD-NTase / HORMA domain / closure motif
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
: / Bacterial HORMA domain / Bacterial HORMA domain 2 / Second Messenger Oligonucleotide or Dinucleotide Synthetase domain / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / HORMA domain superfamily / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CBASS oligonucleotide cyclase / CD-NTase-associated protein 7 / Cyclic AMP-AMP-AMP synthase / HORMA domain containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.893 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 8, 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 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleotidyltransferase
B: HORMA domain containing protein
C: Peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9484
Polymers53,9243
Non-polymers241
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.087, 43.373, 63.217
Angle α, β, γ (deg.)90.00, 104.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nucleotidyltransferase / Nucleotidyltransferase domain protein


Mass: 34063.328 Da / Num. of mol.: 1
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: Protein HORMA domain containing protein


Mass: 18723.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: ORF C60, CAZ10_14260, DY940_15620, DY979_07580, EGY23_20890, EQH76_12140, IPC669_24875, PA5486_02901, PAERUG_E15_London_28_01_14_04350, PAMH19_6113
Production host: Escherichia coli (E. coli) / References: UniProt: Q8GQ50, UniProt: P0DTF6*PLUS
#3: Protein/peptide Peptide 1


Mass: 1137.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Bis-Tris pH 5.5, 0.2 M ammonium acetate, and 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.89→81.97 Å / Num. obs: 34946 / % possible obs: 97.7 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.086 / Rrim(I) all: 0.159 / Net I/σ(I): 7.1
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.302 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1989 / CC1/2: 0.409 / Rpim(I) all: 0.837 / Rrim(I) all: 1.554 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P82, 6P8R

6p82

6p8r


Resolution: 1.893→81.966 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 24.39
RfactorNum. reflection% reflection
Rfree0.2232 1704 4.89 %
Rwork0.1891 --
obs0.1907 34881 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.893→81.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 1 307 4070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053852
X-RAY DIFFRACTIONf_angle_d0.5865213
X-RAY DIFFRACTIONf_dihedral_angle_d11.5462285
X-RAY DIFFRACTIONf_chiral_restr0.041553
X-RAY DIFFRACTIONf_plane_restr0.003673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8928-1.94850.34971310.32612482X-RAY DIFFRACTION88
1.9485-2.01140.31671430.28822770X-RAY DIFFRACTION99
2.0114-2.08330.33871440.2652785X-RAY DIFFRACTION98
2.0833-2.16670.28481350.24022763X-RAY DIFFRACTION98
2.1667-2.26530.2671530.222742X-RAY DIFFRACTION97
2.2653-2.38470.25381470.20262780X-RAY DIFFRACTION99
2.3847-2.53420.25331500.20752812X-RAY DIFFRACTION99
2.5342-2.72980.26011450.20492791X-RAY DIFFRACTION98
2.7298-3.00460.25121520.20392717X-RAY DIFFRACTION97
3.0046-3.43930.21891330.18932832X-RAY DIFFRACTION99
3.4393-4.33320.17561340.14612801X-RAY DIFFRACTION97
4.3332-82.0430.16161370.15352902X-RAY DIFFRACTION98
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)
10.7730.0233-0.5360.42340.39451.7226-0.07990.114-0.0291-0.08560.02060.01220.0660.00760.05840.2226-0.0244-0.0190.19230.03520.2352-30.61936.128715.3436
21.9762-0.49590.5731.4445-0.08492.00610.0172-0.10420.07690.09710.0497-0.1547-0.1060.1556-0.0710.2296-0.02630.00120.2377-0.00020.2459-23.337324.830645.1354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B

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