[English] 日本語
Yorodumi
- PDB-6uxf: Structure of V. metoecus NucC, hexamer form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uxf
TitleStructure of V. metoecus NucC, hexamer form
ComponentsVibrio meotecus sp. RC341 NucC
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 / CRISPR-associated endodeoxyribonuclease NucC
Function and homology information
Biological speciesVibrio metoecus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsYe, Q. / 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
DepositionNov 7, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vibrio meotecus sp. RC341 NucC


Theoretical massNumber of molelcules
Total (without water)28,0721
Polymers28,0721
Non-polymers00
Water5,170287
1
A: Vibrio meotecus sp. RC341 NucC
x 6


Theoretical massNumber of molelcules
Total (without water)168,4326
Polymers168,4326
Non-polymers00
Water1086
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_554-y,-x,-z-1/21
crystal symmetry operation11_654-x+y+1,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area22700 Å2
ΔGint-128 kcal/mol
Surface area55120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.880, 134.880, 85.894
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

21A-508-

HOH

-
Components

#1: Protein Vibrio meotecus sp. RC341 NucC


Mass: 28072.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio metoecus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0DUD6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.02 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.1 M sodium formate, 14% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.65→100 Å / Num. obs: 55873 / % possible obs: 98.5 % / Redundancy: 33.5 % / Biso Wilson estimate: 28.28 Å2 / CC1/2: 1 / Rrim(I) all: 0.066 / Rsym value: 0.065 / Net I/σ(I): 38.7
Reflection shellResolution: 1.65→1.75 Å / Mean I/σ(I) obs: 1.85 / Num. unique obs: 8767 / CC1/2: 0.669 / Rrim(I) all: 1.57 / Rsym value: 1.527

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P7O

6p7o


Resolution: 1.65→69.2 Å / SU ML: 0.1941 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.8837
RfactorNum. reflection% reflection
Rfree0.1843 2886 5.17 %
Rwork0.1731 --
obs0.1736 55839 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.45 Å2
Refinement stepCycle: LAST / Resolution: 1.65→69.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 0 287 2221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01351996
X-RAY DIFFRACTIONf_angle_d1.17352708
X-RAY DIFFRACTIONf_chiral_restr0.0796297
X-RAY DIFFRACTIONf_plane_restr0.0082351
X-RAY DIFFRACTIONf_dihedral_angle_d12.67011191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.39151300.34222363X-RAY DIFFRACTION95.88
1.67-1.70.32361200.2712492X-RAY DIFFRACTION99.13
1.7-1.730.26291450.24742462X-RAY DIFFRACTION99.77
1.73-1.770.24381530.22372474X-RAY DIFFRACTION100
1.77-1.80.19551270.19782505X-RAY DIFFRACTION99.96
1.8-1.840.19941090.17972510X-RAY DIFFRACTION99.92
1.84-1.880.19591540.17562479X-RAY DIFFRACTION99.96
1.88-1.930.19271430.17852503X-RAY DIFFRACTION99.96
1.93-1.980.21621540.1782467X-RAY DIFFRACTION99.96
1.98-2.040.18141200.15962519X-RAY DIFFRACTION100
2.04-2.110.17291330.16142514X-RAY DIFFRACTION100
2.11-2.180.16151630.15032480X-RAY DIFFRACTION100
2.18-2.270.18521490.1422492X-RAY DIFFRACTION100
2.27-2.370.1671300.14662533X-RAY DIFFRACTION100
2.37-2.50.17441280.1462535X-RAY DIFFRACTION99.96
2.5-2.660.17051340.15622536X-RAY DIFFRACTION100
2.66-2.860.18521440.16222554X-RAY DIFFRACTION100
2.86-3.150.19081260.16612560X-RAY DIFFRACTION100
3.15-3.610.15611260.1572590X-RAY DIFFRACTION99.96
3.61-4.540.16041420.15672621X-RAY DIFFRACTION100
4.54-69.20.20241560.21562764X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 46.9509903729 Å / Origin y: -42.2455099475 Å / Origin z: -3.81082839784 Å
111213212223313233
T0.172308136557 Å2-0.010687230078 Å20.0198809279943 Å2-0.211219069022 Å20.00513450058811 Å2--0.183407920713 Å2
L0.878599018512 °2-0.0798922621814 °20.0569569522616 °2-1.43496282351 °2-0.242594070522 °2--0.835048110619 °2
S0.0295387787703 Å °-0.0701569260247 Å °-0.0038530395542 Å °0.0476640655816 Å °0.0187330030994 Å °0.175077222143 Å °-0.0273926373659 Å °-0.105273872564 Å °-0.0530987669625 Å °
Refinement TLS groupSelection details: chain A

+
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://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