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- PDB-6p7q: Structure of E. coli MS115-1 NucC, 5'-pApA bound form -

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Basic information

Entry
Database: PDB / ID: 6p7q
TitleStructure of E. coli MS115-1 NucC, 5'-pApA bound form
Components
  • E. coli MS115-1 NucC
  • RNA (5'-R(P*AP*A)-3')
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: 1.66 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
B: E. coli MS115-1 NucC
C: E. coli MS115-1 NucC
D: RNA (5'-R(P*AP*A)-3')
E: RNA (5'-R(P*AP*A)-3')
F: RNA (5'-R(P*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5657
Polymers82,5296
Non-polymers351
Water16,862936
1
A: E. coli MS115-1 NucC
C: E. coli MS115-1 NucC
D: RNA (5'-R(P*AP*A)-3')
F: RNA (5'-R(P*AP*A)-3')
hetero molecules

A: E. coli MS115-1 NucC
C: E. coli MS115-1 NucC
D: RNA (5'-R(P*AP*A)-3')
F: RNA (5'-R(P*AP*A)-3')
hetero molecules

A: E. coli MS115-1 NucC
C: E. coli MS115-1 NucC
D: RNA (5'-R(P*AP*A)-3')
F: RNA (5'-R(P*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,16515
Polymers165,05912
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
E: RNA (5'-R(P*AP*A)-3')

B: E. coli MS115-1 NucC
E: RNA (5'-R(P*AP*A)-3')

B: E. coli MS115-1 NucC
E: RNA (5'-R(P*AP*A)-3')

B: E. coli MS115-1 NucC
E: RNA (5'-R(P*AP*A)-3')

B: E. coli MS115-1 NucC
E: RNA (5'-R(P*AP*A)-3')

B: E. coli MS115-1 NucC
E: RNA (5'-R(P*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)165,05912
Polymers165,05912
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)131.781, 131.781, 252.836
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

21A-648-

HOH

31B-493-

HOH

41C-447-

HOH

51D-106-

HOH

61E-104-

HOH

71F-106-

HOH

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Components

#1: Protein E. coli MS115-1 NucC


Mass: 26896.377 Da / Num. of mol.: 3 / Mutation: 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 RNA (5'-R(P*AP*A)-3')


Mass: 613.454 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Escherichia coli MS 115-1 (bacteria)
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 936 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
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: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.66→104.02 Å / Num. obs: 98697 / % possible obs: 99.2 % / Redundancy: 5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.066 / Rrim(I) all: 0.154 / Net I/σ(I): 9.7
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.83 / Num. unique obs: 4794 / CC1/2: 0.617 / Rpim(I) all: 0.401 / Rrim(I) all: 0.924 / % possible all: 97.6

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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: 1.66→55.663 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 18.42
RfactorNum. reflection% reflection
Rfree0.1846 4840 4.91 %
Rwork0.1588 --
obs0.1601 98601 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.66→55.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5657 135 1 936 6729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125998
X-RAY DIFFRACTIONf_angle_d1.0258172
X-RAY DIFFRACTIONf_dihedral_angle_d11.2193494
X-RAY DIFFRACTIONf_chiral_restr0.066876
X-RAY DIFFRACTIONf_plane_restr0.0091045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6591-1.67790.29091460.26213033X-RAY DIFFRACTION96
1.6779-1.69770.29771800.25213082X-RAY DIFFRACTION99
1.6977-1.71840.26771690.24383118X-RAY DIFFRACTION100
1.7184-1.74010.26091620.24573126X-RAY DIFFRACTION100
1.7401-1.7630.27761670.24693114X-RAY DIFFRACTION100
1.763-1.78720.27351610.253093X-RAY DIFFRACTION99
1.7872-1.81270.25081790.23922995X-RAY DIFFRACTION96
1.8127-1.83980.27911700.23993124X-RAY DIFFRACTION99
1.8398-1.86850.23291650.2253114X-RAY DIFFRACTION100
1.8685-1.89920.25451510.20933137X-RAY DIFFRACTION100
1.8992-1.93190.24051560.19573166X-RAY DIFFRACTION100
1.9319-1.96710.22181590.17743155X-RAY DIFFRACTION100
1.9671-2.00490.20251870.17653079X-RAY DIFFRACTION100
2.0049-2.04580.21031660.16683128X-RAY DIFFRACTION100
2.0458-2.09030.18681510.16283159X-RAY DIFFRACTION100
2.0903-2.13890.20671520.16333155X-RAY DIFFRACTION100
2.1389-2.19240.18771460.15873166X-RAY DIFFRACTION100
2.1924-2.25170.18231900.1433107X-RAY DIFFRACTION100
2.2517-2.3180.17331480.14173192X-RAY DIFFRACTION100
2.318-2.39280.16531690.13563119X-RAY DIFFRACTION100
2.3928-2.47830.14861440.13643172X-RAY DIFFRACTION100
2.4783-2.57750.17671440.14122966X-RAY DIFFRACTION94
2.5775-2.69480.17341850.14633132X-RAY DIFFRACTION100
2.6948-2.83690.21410.14343174X-RAY DIFFRACTION100
2.8369-3.01460.18511500.14743165X-RAY DIFFRACTION99
3.0146-3.24740.16071560.14723185X-RAY DIFFRACTION99
3.2474-3.57410.14651730.13883141X-RAY DIFFRACTION99
3.5741-4.09120.15311600.1293164X-RAY DIFFRACTION99
4.0912-5.15390.12361540.12323063X-RAY DIFFRACTION95
5.1539-55.69410.20191590.17643237X-RAY DIFFRACTION96
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)
10.26130.19530.11170.24990.15510.19650.00840.0314-0.0278-0.0332-0.0011-0.0455-0.02230.0068-00.12670.00230.00890.1305-0.00150.148720.30160.489829.3789
20.43990.054-0.18080.1501-0.08330.17410.01020.0290.06580.00390.01050.0234-0.0142-0.0199-00.14690.0055-0.00130.14180.00370.130950.044-25.302525.1079
30.23030.10020.05810.46640.17740.2125-0.0075-0.0203-0.04570.05080.0209-0.0820.02870.0428-00.14780.0114-0.00590.15820.0050.14114.9478-13.645163.2795
40.0640.04360.00090.0455-0.00660.0018-0.01950.0577-0.00450.00060.0010.02220.0199-0.0121-0.03120.0835-0.01260.01510.0515-0.00040.06262.37990.158817.2803
50.02340.00820.00530.04630.0010.00170.0050.0164-0.0172-0.0326-0.0258-0.01860.01430.0151-0.00720.0795-0.0065-0.01070.07780.01850.059363.9459-36.655912.9794
60.02720.00270.00890.0192-0.01310.01-0.0053-0.05670.00060.01370.01770.03220.00020.00740.03030.1185-0.0171-0.0360.07550.00030.05671.7199-1.684175.5723
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

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