[English] 日本語
Yorodumi
- PDB-7zgv: Serratia NucC bound to cA3 -

+
Open data


ID or keywords:

Loading...

-
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 / homologyACETATE ION / RNA / Restriction endonuclease
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more