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- PDB-6p8r: Structure of P. aeruginosa ATCC27853 HORMA2 -

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Basic information

Entry
Database: PDB / ID: 6p8r
TitleStructure of P. aeruginosa ATCC27853 HORMA2
ComponentsHORMA domain containing protein
KeywordsPROTEIN BINDING / HORMA domain / CD-NTase / cGAS
Function / homologyBacterial HORMA domain / Bacterial HORMA domain 2 / HORMA domain superfamily / defense response to virus / PHOSPHATE ION / CD-NTase-associated protein 7 / HORMA domain containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.141 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 7, 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 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HORMA domain containing protein
B: HORMA domain containing protein
C: HORMA domain containing protein
D: HORMA domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6476
Polymers75,4574
Non-polymers1902
Water2,738152
1
A: HORMA domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9592
Polymers18,8641
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HORMA domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9592
Polymers18,8641
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HORMA domain containing protein


Theoretical massNumber of molelcules
Total (without water)18,8641
Polymers18,8641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HORMA domain containing protein


Theoretical massNumber of molelcules
Total (without water)18,8641
Polymers18,8641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.106, 106.106, 74.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
HORMA domain containing protein


Mass: 18864.143 Da / Num. of mol.: 4 / Mutation: N-terminal SNA
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
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Imidazole pH 8.0, 0.8 M NaH2PO4, and 0.55-0.8 M KH2PO4

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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: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.14→106.11 Å / Num. obs: 45579 / % possible obs: 99.3 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.028 / Rrim(I) all: 0.07 / Net I/σ(I): 22.6
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.402 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3448 / CC1/2: 0.516 / Rpim(I) all: 0.588 / Rrim(I) all: 1.524 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.141→61.13 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.86
RfactorNum. reflection% reflection
Rfree0.2326 2289 5.03 %
Rwork0.2025 --
obs0.2041 45519 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.141→61.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5207 0 10 152 5369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035339
X-RAY DIFFRACTIONf_angle_d0.5667247
X-RAY DIFFRACTIONf_dihedral_angle_d11.0273111
X-RAY DIFFRACTIONf_chiral_restr0.04796
X-RAY DIFFRACTIONf_plane_restr0.003894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1408-2.18740.29761040.29832380X-RAY DIFFRACTION88
2.1874-2.23830.29941500.28512739X-RAY DIFFRACTION100
2.2383-2.29430.31331520.27232671X-RAY DIFFRACTION100
2.2943-2.35630.28851500.26122714X-RAY DIFFRACTION100
2.3563-2.42560.26481480.25262680X-RAY DIFFRACTION100
2.4256-2.50390.2731550.24432718X-RAY DIFFRACTION100
2.5039-2.59340.3141530.24372709X-RAY DIFFRACTION100
2.5934-2.69730.27981230.24742724X-RAY DIFFRACTION100
2.6973-2.820.3081250.24672734X-RAY DIFFRACTION100
2.82-2.96870.28441320.26192714X-RAY DIFFRACTION100
2.9687-3.15470.30241320.23522748X-RAY DIFFRACTION100
3.1547-3.39820.24211280.21682738X-RAY DIFFRACTION100
3.3982-3.74020.2341640.1982709X-RAY DIFFRACTION100
3.7402-4.28130.1921430.1672732X-RAY DIFFRACTION100
4.2813-5.39340.18271440.16072778X-RAY DIFFRACTION100
5.3934-61.15480.22011860.19442742X-RAY DIFFRACTION100
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)
12.1360.1646-0.29972.82120.76212.8801-0.0248-0.1970.44120.21330.0641-0.3667-0.0792-0.1902-0.04130.55130.114-0.0520.56730.01590.619526.772643.112353.6124
22.1205-0.5039-0.10062.81820.66082.45830.15830.17470.5557-0.1857-0.0646-0.5761-0.0510.1125-0.03710.51050.0172-0.0060.54070.08970.730233.654637.182226.2203
33.8240.89240.39852.2936-0.53351.89710.0944-0.3222-0.2396-0.0733-0.1023-0.1214-0.0357-0.4033-0.06040.50480.07480.04270.8670.07230.47810.929268.514936.0712
44.0159-0.4134-1.41071.8805-0.54742.80210.08080.2810.3025-0.1243-0.1149-0.0876-0.0689-0.32020.02960.54310.002-0.09510.6819-0.04850.5587-0.285139.192826.0889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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