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- PDB-7zgv: Serratia NucC bound to cA3 -

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Basic information

Entry
Database: PDB / ID: 7zgv
TitleSerratia NucC bound to cA3
Components
  • RNA (5'-R(P*AP*AP*A)-3')
  • Serratia NucC
KeywordsRNA BINDING PROTEIN / Nuclease
Function / homologyDomain of unknown function DUF6602 / Domain of unknown function (DUF6602) / ACETATE ION / RNA / DUF6602 domain-containing protein
Function and homology information
Biological speciesSerratia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsGarcia-Doval, C. / Mayo-Munoz, D. / Smith, L.M. / Fineran, P.C.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden FundMFP-UOO2011 New Zealand
CitationJournal: Mol.Cell / Year: 2022
Title: Type III CRISPR-Cas provides resistance against nucleus-forming jumbo phages via abortive infection.
Authors: Mayo-Munoz, D. / Smith, L.M. / Garcia-Doval, C. / Malone, L.M. / Harding, K.R. / Jackson, S.A. / Hampton, H.G. / Fagerlund, R.D. / Gumy, L.F. / Fineran, P.C.
History
DepositionApr 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serratia NucC
D: RNA (5'-R(P*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0386
Polymers29,8392
Non-polymers1984
Water4,342241
1
A: Serratia NucC
D: RNA (5'-R(P*AP*AP*A)-3')
hetero molecules

A: Serratia NucC
D: RNA (5'-R(P*AP*AP*A)-3')
hetero molecules

A: Serratia NucC
D: RNA (5'-R(P*AP*AP*A)-3')
hetero molecules

A: Serratia NucC
D: RNA (5'-R(P*AP*AP*A)-3')
hetero molecules

A: Serratia NucC
D: RNA (5'-R(P*AP*AP*A)-3')
hetero molecules

A: Serratia NucC
D: RNA (5'-R(P*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,22636
Polymers179,03612
Non-polymers1,18924
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_676x-y+1,-y+2,-z+11
crystal symmetry operation6_766-x+2,-x+y+1,-z+11
Unit cell
Length a, b, c (Å)114.265, 114.265, 96.069
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

21A-625-

HOH

31A-632-

HOH

41A-634-

HOH

51A-635-

HOH

61D-106-

HOH

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Components

#1: Protein Serratia NucC


Mass: 28896.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia (bacteria) / Gene: CWC46_19930, Ser39006_019925 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I5TBB8
#2: RNA chain RNA (5'-R(P*AP*AP*A)-3')


Mass: 942.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Serratia (bacteria)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 7.5 0.2 M calcium acetate 25% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→43.21 Å / Num. obs: 40117 / % possible obs: 100 % / Redundancy: 19.9 % / Biso Wilson estimate: 15.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.027 / Net I/σ(I): 17.6
Reflection shellResolution: 1.48→1.506 Å / Rmerge(I) obs: 1.517 / Num. unique obs: 1987 / CC1/2: 0.773 / Rpim(I) all: 0.354

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSBUILT=20190806data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q1H

6q1h


Resolution: 1.48→34.85 Å / SU ML: 0.1434 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9157
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1811 1962 4.89 %
Rwork0.1579 38150 -
obs0.159 40112 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.48 Å2
Refinement stepCycle: LAST / Resolution: 1.48→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 66 10 241 2271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01052070
X-RAY DIFFRACTIONf_angle_d1.13312815
X-RAY DIFFRACTIONf_chiral_restr0.0797321
X-RAY DIFFRACTIONf_plane_restr0.0109354
X-RAY DIFFRACTIONf_dihedral_angle_d13.8785767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.520.23191330.22662684X-RAY DIFFRACTION99.96
1.52-1.560.2371420.21042738X-RAY DIFFRACTION100
1.56-1.60.22391530.20232657X-RAY DIFFRACTION100
1.6-1.660.2161400.18372719X-RAY DIFFRACTION100
1.66-1.720.22721430.18512695X-RAY DIFFRACTION100
1.72-1.780.21331410.17712709X-RAY DIFFRACTION99.96
1.78-1.860.19471400.16252720X-RAY DIFFRACTION100
1.87-1.960.17671350.15652706X-RAY DIFFRACTION100
1.96-2.090.16411380.15422729X-RAY DIFFRACTION100
2.09-2.250.16151210.14092727X-RAY DIFFRACTION100
2.25-2.470.18171430.14512732X-RAY DIFFRACTION100
2.47-2.830.17531400.15522737X-RAY DIFFRACTION100
2.83-3.570.19731500.15032754X-RAY DIFFRACTION100
3.57-34.850.14661430.14882843X-RAY DIFFRACTION99.93
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)
11.89914570787-1.046388890190.6393462848141.48080251966-0.4965368865070.5750150935510.05238353027870.0817014626314-0.120709350293-0.137523237771-0.02574961282540.05552921781470.06663524562530.00210352031413-0.03480292797960.14141434258-0.0127995932632-0.007753668682120.123682644837-0.03674862078110.13513369290453.013936969578.850799582427.5259198359
20.3413398486150.0265458469172-0.05237596212550.3029472030430.1095087513780.0508887227920.0198214427829-0.04789105340870.05032634232510.0114526682814-0.004683999893280.00356090917728-0.0632281715291-0.003378552043440.1226940816450.1111466875630.004343828823430.002158491658840.0423171149373-0.01534855249390.03710070234957.109588795598.947625590120.8579786466
30.3826354987870.587731501462-0.5887214836581.43478040864-0.4967559466351.220069454020.0157951632554-0.18418266006-0.120866417669-0.00434608115686-0.0277635271246-0.2024776274740.007049674703190.184371371098-0.0490469396750.1015558660510.00457869485018-0.01055591293470.123916935492-0.004759340836210.14875651257770.513736502875.720429562244.9282355221
40.606013952972-0.1137555186020.0854664326861.13202427036-0.5056356109060.68064105520.00191108630928-0.00786715374349-0.0906756506982-0.01597549944970.04147650707920.0586387665480.0407681297273-0.0499939738081-0.04491363545730.106742810446-0.00331922650283-0.01283465348350.109281614908-0.01165755316570.1345101018347.373533155983.230101364233.3014341657
55.826386564860.1910754412320.4109895100235.580209816040.933448624563.80187776121-0.03489542020570.572850966275-1.0191766324-0.609343276914-0.07183083750140.3114348351461.25313090017-0.0811925896807-0.1023877032440.443397819755-0.01185924517850.005496404271130.239879568315-0.08236966496060.47596510402354.920769926560.302199105832.2730537683
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 186 through 250 )AA186 - 250182 - 246
22chain 'D' and (resid 1 through 3 )DB1 - 3
33chain 'A' and (resid 5 through 38 )AA5 - 381 - 34
44chain 'A' and (resid 39 through 165 )AA39 - 16535 - 161
55chain 'A' and (resid 166 through 185 )AA166 - 185162 - 181

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