[English] 日本語
Yorodumi
- PDB-6sf4: Apo form of the ribonucleotide reductase NrdB protein from Leeuwe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sf4
TitleApo form of the ribonucleotide reductase NrdB protein from Leeuwenhoekiella blandensis
ComponentsRibonucleoside-diphosphate reductase, beta subunit 1
KeywordsMETAL BINDING PROTEIN / ribonucleotide reductase apoprotein manganese binding redox protein deoxyribonucleotide synthesis
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily ...ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesLeeuwenhoekiella blandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHasan, M. / Rozman Grinberg, I. / Sjoberg, B.M. / Logan, D.T.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2016-04855 Sweden
Swedish Research Council2016-01920 Sweden
Wenner-Gren Foundation Sweden
CitationJournal: J.Biol.Inorg.Chem. / Year: 2019
Title: Class Id ribonucleotide reductase utilizes a Mn2(IV,III) cofactor and undergoes large conformational changes on metal loading.
Authors: Rozman Grinberg, I. / Berglund, S. / Hasan, M. / Lundin, D. / Ho, F.M. / Magnuson, A. / Logan, D.T. / Sjoberg, B.M. / Berggren, G.
History
DepositionJul 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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: Ribonucleoside-diphosphate reductase, beta subunit 1
B: Ribonucleoside-diphosphate reductase, beta subunit 1


Theoretical massNumber of molelcules
Total (without water)81,1562
Polymers81,1562
Non-polymers00
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-17 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.587, 68.196, 148.235
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ribonucleoside-diphosphate reductase, beta subunit 1


Mass: 40577.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leeuwenhoekiella blandensis (strain CECT 7118 / CCUG 51940 / MED217) (bacteria)
Strain: CECT 7118 / CCUG 51940 / MED217 / Gene: MED217_17135 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): /pET28a(+)
References: UniProt: A3XHF9, ribonucleoside-diphosphate reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein at 7.5 mg/ml in buffer containing 50 mM Tris-HCl pH 7.8, 300 mM NaCl, 10% glycerol, 20 mM MgCl2 and 2 mM tris(2-carboxyethyl)phosphine (TCEP). Precipitant 2.4 M sodium malonate ...Details: Protein at 7.5 mg/ml in buffer containing 50 mM Tris-HCl pH 7.8, 300 mM NaCl, 10% glycerol, 20 mM MgCl2 and 2 mM tris(2-carboxyethyl)phosphine (TCEP). Precipitant 2.4 M sodium malonate dibasic monohydrate pH 7.0. Drops 200+200 nl.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.85 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.7→49.94 Å / Num. obs: 74093 / % possible obs: 97.5 % / Redundancy: 17.5 % / Biso Wilson estimate: 32.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.035 / Net I/σ(I): 14.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 14.8 % / Rmerge(I) obs: 2.299 / Mean I/σ(I) obs: 1 / Num. unique obs: 3025 / CC1/2: 0.538 / Rpim(I) all: 0.854 / % possible all: 76.2

-
Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SYY

1syy


Resolution: 1.7→49.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.096 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.091 / SU Rfree Cruickshank DPI: 0.089
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3669 -RANDOM
Rwork0.175 ---
obs0.176 74037 97.3 %-
Displacement parametersBiso mean: 35.15 Å2
Baniso -1Baniso -2Baniso -3
1-7.4468 Å20 Å20 Å2
2---0.846 Å20 Å2
3----6.6007 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.7→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4885 0 0 486 5371

+
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