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- PDB-6q1h: Structure of P. aeruginosa ATCC27853 NucC, cAAA-bound form -

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Basic information

Entry
Database: PDB / ID: 6q1h
TitleStructure of P. aeruginosa ATCC27853 NucC, cAAA-bound form
Components
  • Bacterial protein ORF C62
  • RNA (5'-R(P*AP*AP*A)-3')
KeywordsDNA BINDING PROTEIN/RNA / Nuclease / DNA BINDING PROTEIN / DNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / nucleotide binding / metal ion binding
Similarity search - Function
Domain of unknown function DUF6602 / Domain of unknown function (DUF6602)
Similarity search - Domain/homology
RNA / Endodeoxyribonuclease NucC / Uncharacterized protein ORF C62
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsYe, Q. / Lau, R.K. / Corbett, K.D.
CitationJournal: Mol.Cell / Year: 2020
Title: Structure and Mechanism of a Cyclic Trinucleotide-Activated Bacterial Endonuclease Mediating Bacteriophage Immunity.
Authors: Lau, R.K. / Ye, Q. / Birkholz, E.A. / Berg, K.R. / Patel, L. / Mathews, I.T. / Watrous, J.D. / Ego, K. / Whiteley, A.T. / Lowey, B. / Mekalanos, J.J. / Kranzusch, P.J. / Jain, M. / Pogliano, J. / Corbett, K.D.
History
DepositionAug 4, 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.year
Revision 1.2Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 4, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Oct 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

Downloads & links

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Assembly

Deposited unit
A: Bacterial protein ORF C62
B: Bacterial protein ORF C62
C: Bacterial protein ORF C62
D: RNA (5'-R(P*AP*AP*A)-3')
E: Bacterial protein ORF C62
F: Bacterial protein ORF C62
G: Bacterial protein ORF C62
H: RNA (5'-R(P*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)162,0148
Polymers162,0148
Non-polymers00
Water37,0752058
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Confirmed by size exclusion chromatography coupled to multi-angle light scattering (SEC-MALS)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.498, 80.450, 262.078
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Bacterial protein ORF C62


Mass: 26688.146 Da / Num. of mol.: 6 / Mutation: D73N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ORF C62 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GQ48, UniProt: P0DTF8*PLUS
#2: RNA chain RNA (5'-R(P*AP*AP*A)-3')


Mass: 942.660 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2058 / 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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M HEPES pH 7.5, 0.1 M L-proline, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.45→100 Å / Num. obs: 293192 / % possible obs: 97.1 % / Redundancy: 12.1 % / Biso Wilson estimate: 16.83 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.087 / Net I/σ(I): 20.4
Reflection shellResolution: 1.45→1.54 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.261 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 40591 / CC1/2: 0.499 / Rrim(I) all: 1.368 / % possible all: 83.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P7O

6p7o


Resolution: 1.45→76.95 Å / SU ML: 0.1676 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.557
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.167 14679 5.01 %
Rwork0.1471 278094 -
obs0.1481 292773 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.02 Å2
Refinement stepCycle: LAST / Resolution: 1.45→76.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11250 132 0 2058 13440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008711839
X-RAY DIFFRACTIONf_angle_d1.060116182
X-RAY DIFFRACTIONf_chiral_restr0.07961785
X-RAY DIFFRACTIONf_plane_restr0.00722083
X-RAY DIFFRACTIONf_dihedral_angle_d17.15984236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.37234250.35427219X-RAY DIFFRACTION76.96
1.47-1.480.34434090.3247759X-RAY DIFFRACTION82.48
1.48-1.50.3383900.30738248X-RAY DIFFRACTION86.87
1.5-1.520.28294760.27668545X-RAY DIFFRACTION90.5
1.52-1.540.28814290.25848741X-RAY DIFFRACTION92.92
1.54-1.560.26995010.24158955X-RAY DIFFRACTION95.2
1.56-1.580.2415110.22019222X-RAY DIFFRACTION97.85
1.58-1.610.23464590.19499513X-RAY DIFFRACTION99.97
1.61-1.630.21724410.18029435X-RAY DIFFRACTION99.97
1.63-1.660.19024760.16819460X-RAY DIFFRACTION99.98
1.66-1.690.1934880.16779445X-RAY DIFFRACTION100
1.69-1.720.18595000.16699517X-RAY DIFFRACTION100
1.72-1.750.20145400.16189438X-RAY DIFFRACTION99.98
1.75-1.790.18444650.15829478X-RAY DIFFRACTION99.93
1.79-1.830.18554760.15499487X-RAY DIFFRACTION99.97
1.83-1.870.17845490.14789443X-RAY DIFFRACTION99.97
1.87-1.920.16785300.14839451X-RAY DIFFRACTION100
1.92-1.970.16875150.13819423X-RAY DIFFRACTION99.95
1.97-2.030.16495080.13469494X-RAY DIFFRACTION99.99
2.03-2.090.15445360.13229449X-RAY DIFFRACTION99.96
2.09-2.170.15724500.12819554X-RAY DIFFRACTION100
2.17-2.250.14525090.12119504X-RAY DIFFRACTION99.95
2.25-2.360.14065170.11889546X-RAY DIFFRACTION99.99
2.36-2.480.15565030.12179518X-RAY DIFFRACTION100
2.48-2.630.14274980.12649546X-RAY DIFFRACTION100
2.63-2.840.14435140.13199589X-RAY DIFFRACTION99.97
2.84-3.120.14825180.13039627X-RAY DIFFRACTION99.99
3.12-3.580.14685040.13019660X-RAY DIFFRACTION100
3.58-4.510.14235070.12489788X-RAY DIFFRACTION99.99
4.51-77.060.1635350.163610040X-RAY DIFFRACTION99.57
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)
10.7242020271210.186921306723-0.03795571902230.4492598532130.01102555082440.419714313790.0179215739739-0.104525886881-0.02474620577670.0772310280671-0.0129535207349-0.05392437902490.02991640842710.0615850126376-0.0001627725101670.1348386274430.0196469485228-0.008755612451030.1147396804090.01359817501520.105051930331-13.2871741628-17.2693703048-14.3515453842
20.674564053981-0.1163545545660.295249548870.600709185473-0.224978159790.5479042487560.02794040922830.1692389893830.00737952386744-0.121003477019-0.0407179192516-0.05308475453040.07551514361040.1541536433-0.003026941783340.1261544455170.02759889747490.02243768960190.13239335865-0.0114181834350.103466027121-9.31435273553-17.7984440784-48.77326887
30.329507223908-0.09308294195280.00522696802980.6588175640640.2785085957790.789366073533-0.00307005870760.00249438576732-0.02345255556690.0092040172781-0.03187002823530.1341806816710.00734146857064-0.157471567454-0.0004992997344950.10900222509-0.00105617564456-0.008638890266410.1152346194920.004270871110930.13137848275-40.9197534539-15.8002753359-35.0578053669
40.0001398720931260.000953276054855-0.0001443384613690.004636819041130.000191607314016-0.000288533181182-0.001435961972730.0298167136535-0.0587145099406-0.0268054666321-0.0258434282780.05275486487350.0957161511856-0.0372273657116-7.39491993861E-50.1468108471480.00637896355737-0.01310857040140.10333152358-0.0009748975041170.133880256384-21.8709686105-29.1717259652-32.6556170578
50.4473863335710.006784375985260.006280934285080.4846014863920.1387874028490.560131199147-0.01280489267610.06248285397280.012439114397-0.09600788766650.001887588292380.0372376084263-0.0176866237022-0.0439046299353-0.0009736062435880.1078273806760.0141708149111-0.02213576683620.09325332734940.009684360315410.104429405937-32.800113148117.7244020526-47.2780320266
60.461630389472-0.1543740417120.1203555174130.587751894119-0.2434806051150.772870518547-0.002065812897740.04179287983460.0245458063751-0.0298222904243-0.0239037903594-0.1029536875320.04328929840530.149417117-0.001652755968230.09117829352880.003165127456520.01076930736060.124263803676-0.000298355863150.1323175076980.39849850423315.7956962026-37.5783770904
70.5642203133920.1809811058030.004449814381090.4141409507250.003560108279540.3958823946170.0126426829861-0.09213956966810.02735511279310.0805468499857-0.01518238866510.0438307960135-0.0133633479206-0.0412258166942-0.0003715688662050.1130791492370.01683883877430.001038769949120.114058451925-0.01196374270910.10843669212-24.535389889217.4402855365-13.6685826914
8-0.000549190781505-0.0001203543142720.0004874901666380.00770908430018-0.000131107976167-0.001184347448780.004745449619510.0101173053790.0655089724863-0.106006960488-0.050266317442-0.0377508005072-0.1144822636510.016520159532-8.75957555991E-50.1319307797770.00745207245831-0.005790446448770.1097336223660.0008718861099820.145058473907-18.262437034829.2592469418-32.931740724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B
3X-RAY DIFFRACTION3Chain C
4X-RAY DIFFRACTION4Chain D
5X-RAY DIFFRACTION5Chain E
6X-RAY DIFFRACTION6Chain F
7X-RAY DIFFRACTION7Chain G
8X-RAY DIFFRACTION8Chain H

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