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- PDB-6p8p: Structure of P. aeruginosa ATCC27853 HORMA1 -

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Basic information

Entry
Database: PDB / ID: 6p8p
TitleStructure of P. aeruginosa ATCC27853 HORMA1
ComponentsUncharacterized protein
KeywordsPROTEIN BINDING / HORMA domain / CD-NTase
Function / homologydefense response to virus / Type III CBASS phage resistance system CD-NTase-associated protein Cap8 / CD-NTase-associated protein 8
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.635 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0408
Polymers66,8794
Non-polymers1604
Water9,890549
1
A: Uncharacterized protein
hetero molecules

C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)33,4803
Polymers33,4402
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1370 Å2
ΔGint-25 kcal/mol
Surface area12200 Å2
MethodPISA
2
B: Uncharacterized protein
hetero molecules

D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5605
Polymers33,4402
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1370 Å2
ΔGint-24 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.525, 97.525, 60.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11C-403-

HOH

21C-428-

HOH

31C-434-

HOH

41D-381-

HOH

51D-403-

HOH

61D-404-

HOH

71D-409-

HOH

81D-413-

HOH

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Components

#1: Protein
Uncharacterized protein


Mass: 16719.801 Da / Num. of mol.: 4 / Mutation: V102M, L146M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: DY979_07575, EGY23_20885, IPC669_24870, PA5486_02900, PAERUG_E15_London_28_01_14_04349
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6RRN7, UniProt: P0DTF5*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM imidazole pH 8.0, 200 mM CaCl2, and 32% 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: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 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: 1.635→97.53 Å / Num. obs: 69749 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Rrim(I) all: 0.101 / Net I/σ(I): 15
Reflection shellResolution: 1.635→1.66 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.786 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3430 / CC1/2: 0.445 / Rpim(I) all: 0.768 / Rrim(I) all: 1.949 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.635→97.525 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.73
RfactorNum. reflection% reflection
Rfree0.1984 3415 4.9 %
Rwork0.1733 --
obs0.1746 69695 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.635→97.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 4 549 4531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094077
X-RAY DIFFRACTIONf_angle_d0.955538
X-RAY DIFFRACTIONf_dihedral_angle_d11.172488
X-RAY DIFFRACTIONf_chiral_restr0.051630
X-RAY DIFFRACTIONf_plane_restr0.008728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6351-1.65850.32941230.32822592X-RAY DIFFRACTION93
1.6585-1.68320.31321390.29342780X-RAY DIFFRACTION100
1.6832-1.70950.32521360.28852750X-RAY DIFFRACTION100
1.7095-1.73750.31191620.27732721X-RAY DIFFRACTION100
1.7375-1.76750.33371360.24892780X-RAY DIFFRACTION100
1.7675-1.79960.26051560.2422703X-RAY DIFFRACTION100
1.7996-1.83430.24751400.22592750X-RAY DIFFRACTION100
1.8343-1.87170.24471390.21672774X-RAY DIFFRACTION100
1.8717-1.91240.26541430.20682760X-RAY DIFFRACTION100
1.9124-1.95690.22931750.1942699X-RAY DIFFRACTION100
1.9569-2.00580.22441190.19462809X-RAY DIFFRACTION100
2.0058-2.06010.22981490.19812737X-RAY DIFFRACTION100
2.0601-2.12070.24241600.19012767X-RAY DIFFRACTION100
2.1207-2.18920.19481350.17232715X-RAY DIFFRACTION100
2.1892-2.26740.19561520.1612782X-RAY DIFFRACTION100
2.2674-2.35820.19791000.15822794X-RAY DIFFRACTION100
2.3582-2.46550.18661220.16292792X-RAY DIFFRACTION100
2.4655-2.59550.19771390.1592796X-RAY DIFFRACTION100
2.5955-2.75820.22071650.16362744X-RAY DIFFRACTION100
2.7582-2.97110.22141120.17382807X-RAY DIFFRACTION100
2.9711-3.27010.18011640.16512772X-RAY DIFFRACTION100
3.2701-3.74340.1631410.15582784X-RAY DIFFRACTION100
3.7434-4.71620.14661490.13212815X-RAY DIFFRACTION100
4.7162-97.69890.17211590.16742857X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 21.9198 Å / Origin y: 67.9649 Å / Origin z: -16.2428 Å
111213212223313233
T0.1658 Å2-0.0108 Å2-0.0033 Å2-0.1702 Å20.0007 Å2--0.1909 Å2
L-0.0173 °2-0.0386 °2-0.0369 °2--0.0282 °20.0268 °2--0.4318 °2
S-0.006 Å °-0.0169 Å °-0.0142 Å °0.0196 Å °-0.0057 Å °0.003 Å °0.0409 Å °-0.0199 Å °-0.0036 Å °
Refinement TLS groupSelection details: all

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