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- PDB-6p7p: Structure of E. coli MS115-1 NucC, cAAA-bound form -

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Basic information

Entry
Database: PDB / ID: 6p7p
TitleStructure of E. coli MS115-1 NucC, cAAA-bound form
Components
  • Cyclic tri-AMP (5'-3' linked)
  • E. coli MS115-1 NucC 2-241
KeywordsDNA BINDING PROTEIN / nuclease
Function / homologyDomain of unknown function DUF6602 / Domain of unknown function (DUF6602) / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / nucleotide binding / metal ion binding / RNA / Endodeoxyribonuclease NucC
Function and homology information
Biological speciesEscherichia coli MS 115-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.665 Å
AuthorsYe, Q. / Lau, R.K. / Berg, K.R. / 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
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.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: E. coli MS115-1 NucC 2-241
B: E. coli MS115-1 NucC 2-241
C: E. coli MS115-1 NucC 2-241
D: Cyclic tri-AMP (5'-3' linked)
E: Cyclic tri-AMP (5'-3' linked)
F: Cyclic tri-AMP (5'-3' linked)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5537
Polymers83,5176
Non-polymers351
Water15,511861
1
A: E. coli MS115-1 NucC 2-241
C: E. coli MS115-1 NucC 2-241
D: Cyclic tri-AMP (5'-3' linked)
F: Cyclic tri-AMP (5'-3' linked)
hetero molecules

A: E. coli MS115-1 NucC 2-241
C: E. coli MS115-1 NucC 2-241
D: Cyclic tri-AMP (5'-3' linked)
F: Cyclic tri-AMP (5'-3' linked)
hetero molecules

A: E. coli MS115-1 NucC 2-241
C: E. coli MS115-1 NucC 2-241
D: Cyclic tri-AMP (5'-3' linked)
F: Cyclic tri-AMP (5'-3' linked)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,14115
Polymers167,03412
Non-polymers1063
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2
B: E. coli MS115-1 NucC 2-241
E: Cyclic tri-AMP (5'-3' linked)

B: E. coli MS115-1 NucC 2-241
E: Cyclic tri-AMP (5'-3' linked)

B: E. coli MS115-1 NucC 2-241
E: Cyclic tri-AMP (5'-3' linked)

B: E. coli MS115-1 NucC 2-241
E: Cyclic tri-AMP (5'-3' linked)

B: E. coli MS115-1 NucC 2-241
E: Cyclic tri-AMP (5'-3' linked)

B: E. coli MS115-1 NucC 2-241
E: Cyclic tri-AMP (5'-3' linked)


Theoretical massNumber of molelcules
Total (without water)167,03412
Polymers167,03412
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Unit cell
Length a, b, c (Å)131.592, 131.592, 252.109
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-544-

HOH

21B-468-

HOH

31C-448-

HOH

41D-103-

HOH

51E-105-

HOH

61F-103-

HOH

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Components

#1: Protein E. coli MS115-1 NucC 2-241


Mass: 26896.377 Da / Num. of mol.: 3 / Mutation: N-terminal SNA fusion; D73N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli MS 115-1 (bacteria) / Gene: HMPREF9540_01761 / Production host: Escherichia coli (E. coli) / References: UniProt: D7Y2H5
#2: RNA chain Cyclic tri-AMP (5'-3' linked)


Mass: 942.660 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Escherichia coli MS 115-1 (bacteria)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 861 / 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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 17-24% PEG 3350, 0.1 M Na/K tartrate, and 25 mM Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.66→103.85 Å / Num. obs: 97528 / % possible obs: 99.4 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.031 / Rrim(I) all: 0.098 / Net I/σ(I): 20.5
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.601 / Num. unique obs: 4200 / CC1/2: 0.89 / Rpim(I) all: 0.205 / Rrim(I) all: 0.636 / % possible all: 87.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P7O

6p7o


Resolution: 1.665→65.796 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 14.58
RfactorNum. reflection% reflection
Rfree0.1621 4788 4.91 %
Rwork0.1419 --
obs0.1429 97503 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.665→65.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5657 198 1 861 6717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086084
X-RAY DIFFRACTIONf_angle_d0.9688302
X-RAY DIFFRACTIONf_dihedral_angle_d11.2973540
X-RAY DIFFRACTIONf_chiral_restr0.056893
X-RAY DIFFRACTIONf_plane_restr0.0081052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6646-1.68350.24511380.20032517X-RAY DIFFRACTION83
1.6835-1.70330.20571630.17743090X-RAY DIFFRACTION100
1.7033-1.72410.21720.1653048X-RAY DIFFRACTION100
1.7241-1.74590.21141660.16633072X-RAY DIFFRACTION100
1.7459-1.76890.18761600.16113109X-RAY DIFFRACTION100
1.7689-1.79310.21471580.20363069X-RAY DIFFRACTION100
1.7931-1.81880.20311860.18153041X-RAY DIFFRACTION100
1.8188-1.84590.17981710.17453108X-RAY DIFFRACTION100
1.8459-1.87470.22311550.16533045X-RAY DIFFRACTION100
1.8747-1.90550.20781480.16113116X-RAY DIFFRACTION100
1.9055-1.93830.17261530.15563113X-RAY DIFFRACTION100
1.9383-1.97360.19141690.14683064X-RAY DIFFRACTION100
1.9736-2.01160.17471690.14453076X-RAY DIFFRACTION100
2.0116-2.05260.17641600.14283113X-RAY DIFFRACTION100
2.0526-2.09730.17921570.14653119X-RAY DIFFRACTION100
2.0973-2.1460.16171470.14123099X-RAY DIFFRACTION100
2.146-2.19970.17941480.13943106X-RAY DIFFRACTION100
2.1997-2.25920.15351790.13493078X-RAY DIFFRACTION100
2.2592-2.32570.1761470.133095X-RAY DIFFRACTION100
2.3257-2.40070.13931710.12733119X-RAY DIFFRACTION100
2.4007-2.48660.15541460.13153105X-RAY DIFFRACTION100
2.4866-2.58610.15961560.13483132X-RAY DIFFRACTION100
2.5861-2.70380.16171820.13943099X-RAY DIFFRACTION100
2.7038-2.84640.13951260.13853153X-RAY DIFFRACTION100
2.8464-3.02470.16551500.14093136X-RAY DIFFRACTION100
3.0247-3.25820.15241550.14243135X-RAY DIFFRACTION100
3.2582-3.58610.14191720.1313119X-RAY DIFFRACTION100
3.5861-4.10490.13571610.12313165X-RAY DIFFRACTION100
4.1049-5.17150.12351620.11653184X-RAY DIFFRACTION100
5.1715-65.84740.18131610.16743290X-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)
10.61390.41610.26260.66450.33110.42590.0020.076-0.039-0.05120.0131-0.1092-0.030.0577-0.01330.12270.00620.01320.13280.00410.138420.28550.443629.2459
21.34790.2356-0.45460.3747-0.18280.4350.02430.02520.13360.01010.00630.0691-0.0448-0.0628-0.03090.14520.0112-0.00820.13170.00080.123149.9355-25.326825.0078
30.48140.38230.1831.27370.48030.5167-0.0042-0.0378-0.11970.09650.0428-0.20550.10580.096-0.0410.15220.0217-0.00550.16910.01550.14614.842-13.71663.1057
4-0.00050.00010-0.00060.0001-0.0007-0.0014-0.0599-0.09780.0318-0.0299-0.11110.03070.06360.02030.14470.0032-0.04820.1580.07030.1331-0.0106-0.004917.1069
50.12180.1641-0.0570.2204-0.07670.0261-0.0266-0.05850.11010.04820.00690.0748-0.0625-0.0320.01830.14420.0101-0.00280.153-0.05860.102165.7997-37.989812.9093
6-0.0002-00.0001-0.0003-0-0.00050.00120.00660.007-0.05240.0336-0.08090.04720.0512-0.02960.19610.0040.06610.17650.02080.0868-0.00170.001375.3544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 3 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 3 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 3 )

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