[English] 日本語
Yorodumi
- PDB-7ai8: Structure of Ribonucleotide reductase R2 from Escherichia coli co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ai8
TitleStructure of Ribonucleotide reductase R2 from Escherichia coli collected by still serial crystallography on a COC membrane at a synchrotron source
ComponentsRibonucleoside-diphosphate reductase 1 subunit beta
KeywordsOXIDOREDUCTASE / metalloprotein
Function / homology
Function and homology information


ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / iron ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / Ribonucleoside-diphosphate reductase 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAurelius, O. / John, J. / Martiel, I. / Padeste, C. / Karpik, A. / Huang, C.Y. / Hogbom, M. / Wang, M. / Marsh, M.
Funding support Sweden, European Union, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
European Research Council (ERC)HIGH-GEAR 724394European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Versatile microporous polymer-based supports for serial macromolecular crystallography.
Authors: Martiel, I. / Beale, J.H. / Karpik, A. / Huang, C.Y. / Vera, L. / Olieric, N. / Wranik, M. / Tsai, C.J. / Muhle, J. / Aurelius, O. / John, J. / Hogbom, M. / Wang, M. / Marsh, M. / Padeste, C.
History
DepositionSep 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 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: Ribonucleoside-diphosphate reductase 1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6703
Polymers43,5581
Non-polymers1122
Water1,856103
1
A: Ribonucleoside-diphosphate reductase 1 subunit beta
hetero molecules

A: Ribonucleoside-diphosphate reductase 1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3396
Polymers87,1162
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area6660 Å2
ΔGint-81 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.350, 90.350, 208.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

21A-585-

HOH

-
Components

#1: Protein Ribonucleoside-diphosphate reductase 1 subunit beta / Protein B2 / Protein R2 / Ribonucleotide reductase 1


Mass: 43558.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: nrdB, ftsB, b2235, JW2229 / Production host: Escherichia coli (E. coli)
References: UniProt: P69924, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 34-37 % PAA 2100, 100 mM HEPES 7.0, 250-450 mM NaCl, 200 mM ammonium sulfate [and] 26% PAA 2100, 100 mM HEPES 7.0, 150 NaCl, 100 Malonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→52.2 Å / Num. obs: 31083 / % possible obs: 99.65 % / Redundancy: 201.59 % / Biso Wilson estimate: 41.87 Å2 / CC1/2: 0.9967 / CC star: 0.9992 / R split: 0.0538 / Net I/σ(I): 10.74
Reflection shellResolution: 2.1→2.13 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 1.74 / Num. unique obs: 1474 / CC1/2: 0.3829 / CC star: 0.7441 / R split: 0.7483 / % possible all: 96.66
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample holding: COC thin membrane

-
Processing

Software
NameVersionClassification
CrystFEL0.7 / 0.8data reduction
CrystFEL0.7 / 0.8data scaling
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874phasing
Coot0.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MXR

1mxr


Resolution: 2.1→51.97 Å / SU ML: 0.2272 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2192 1505 5 %
Rwork0.19 28589 -
obs0.1914 30094 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.43 Å2
Refinement stepCycle: LAST / Resolution: 2.1→51.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 2 103 2886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692858
X-RAY DIFFRACTIONf_angle_d0.83063879
X-RAY DIFFRACTIONf_chiral_restr0.0455427
X-RAY DIFFRACTIONf_plane_restr0.005499
X-RAY DIFFRACTIONf_dihedral_angle_d22.77011063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.35161300.31282463X-RAY DIFFRACTION97.66
2.17-2.250.29051320.26222527X-RAY DIFFRACTION99.07
2.25-2.340.26361340.23232539X-RAY DIFFRACTION99.33
2.34-2.440.28461330.22382571X-RAY DIFFRACTION99.52
2.44-2.570.26881360.20562549X-RAY DIFFRACTION99.78
2.57-2.730.22571350.20082570X-RAY DIFFRACTION99.74
2.73-2.940.27831360.20822589X-RAY DIFFRACTION100
2.94-3.240.21541380.20272617X-RAY DIFFRACTION99.82
3.24-3.710.2131370.19072607X-RAY DIFFRACTION99.82
3.71-4.670.17631430.15822688X-RAY DIFFRACTION99.89
4.67-51.970.19891510.17352869X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -21.6870560366 Å / Origin y: 29.9104760991 Å / Origin z: 4.74723600776 Å
111213212223313233
T0.58939514316 Å2-0.0814174462062 Å20.146638627644 Å2-0.526722259698 Å2-0.0813009001411 Å2--0.326226468233 Å2
L0.909782715693 °2-0.609732530918 °2-0.339962291214 °2-2.10264206161 °20.721131114001 °2--1.5902201617 °2
S0.0843683493787 Å °-0.0754490865709 Å °0.191436062487 Å °-0.480872376359 Å °0.248750609397 Å °-0.456703427797 Å °-0.224170580876 Å °0.225657690653 Å °-0.267626676632 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 339)

+
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