[English] 日本語
Yorodumi
- PDB-2xo4: RIBONUCLEOTIDE REDUCTASE Y730NH2Y MODIFIED R1 SUBUNIT OF E. COLI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xo4
TitleRIBONUCLEOTIDE REDUCTASE Y730NH2Y MODIFIED R1 SUBUNIT OF E. COLI
Components
  • RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
  • RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
KeywordsOXIDOREDUCTASE / NUCLEOTIDE-BINDING / ALTERNATIVE INITIATION / DNA REPLICATION / ALLOSTERIC ENZYME
Function / homology
Function and homology information


ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / iron ion binding / ATP binding ...ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / iron ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal ...ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / 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 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase 1 subunit alpha / Ribonucleoside-diphosphate reductase 1 subunit beta
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMinnihan, E.C. / Seyedsayamdost, M.R. / Uhlin, U. / Stubbe, J.
Citation
Journal: J.Am.Chem.Soc. / Year: 2011
Title: Kinetics of Radical Intermediate Formation and Deoxynucleotide Production in 3-Aminotyrosine- Substituted Escherichia Coli Ribonucleotide Reductases.
Authors: Minnihan, E.C. / Seyedsayamdost, M.R. / Uhlin, U. / Stubbe, J.
#1: Journal: Nature / Year: 1994
Title: Structure of Ribonucleotide Reductase Protein R1
Authors: Uhlin, U. / Eklund, H.
#2: Journal: Structure / Year: 1997
Title: Binding of Allosteric Effectors to Ribonucleotide Reductase Protein R1: Reduction of Active-Site Cysteines Promotes Substrate Binding
Authors: Eriksson, M. / Uhlin, U. / Ramaswamy, S. / Ekberg, M. / Regnstrom, K. / Sjoberg, B.M. / Eklund, H.
History
DepositionAug 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
B: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
C: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
D: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
E: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
F: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
P: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA


Theoretical massNumber of molelcules
Total (without water)266,7627
Polymers266,7627
Non-polymers00
Water18,1411007
1
C: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
F: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
x 6


Theoretical massNumber of molelcules
Total (without water)528,98112
Polymers528,98112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation6_555-x,-x+y,-z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area28920 Å2
ΔGint-156.4 kcal/mol
Surface area156380 Å2
MethodPISA
2
A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
B: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
D: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
E: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA

A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
B: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
D: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
E: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA

A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
B: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
D: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
E: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA


Theoretical massNumber of molelcules
Total (without water)528,98112
Polymers528,98112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area29660 Å2
ΔGint-152.1 kcal/mol
Surface area156060 Å2
MethodPISA
3
P: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA


  • defined by software
  • 2.27 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2,2711
Polymers2,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)224.592, 224.592, 336.719
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11C-2150-

HOH

21C-2252-

HOH

-
Components

#1: Protein RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA / RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 R1 SUBUNIT / RIBONUCLEOTIDE REDUCTASE 1 / PROTEIN B1 / ...RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 R1 SUBUNIT / RIBONUCLEOTIDE REDUCTASE 1 / PROTEIN B1 / RIBONUCLEOTIDE REDUCTASE R1 SUBUNIT


Mass: 85892.102 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-761
Source method: isolated from a genetically manipulated source
Details: SITE SPECIFIC INCORPORATION OF 3-AMINOTYROSINE AT POSITION 730
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PBADMYCHISA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10
References: UniProt: P00452, ribonucleoside-diphosphate reductase
#2: Protein/peptide
RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA / RIBONUCLEOTIDE REDUCTASE 1 / PROTEIN B2 / PROTEIN R2


Mass: 2271.392 Da / Num. of mol.: 4
Fragment: RIBONUCLEOTIDE REDUCTASE R2-PEPTIDE, RESIDUES 357-376
Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
References: UniProt: P69924, ribonucleoside-diphosphate reductase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1007 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 6
Details: LITHIUM SULPHATE 1.5M, SODIUM CHLORIDE BUFFER PH 6.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.5→84.21 Å / Num. obs: 112261 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 4.47 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.1
Reflection shellResolution: 2.5→2.52 Å / Redundancy: 4.46 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.94 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X0X

2x0x


Resolution: 2.5→169.031 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.084 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.376 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PO4 PO4 BINDING LOOP CONTAINING RESIDUES 268-273 ARE DISORDERED. STRONG INDICATION THAT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PO4 PO4 BINDING LOOP CONTAINING RESIDUES 268-273 ARE DISORDERED. STRONG INDICATION THAT Y731 AND N733 HAVE TWO POSITIONS. THE SECOND POSITION FOR THESE RESIDUES ARE BUILT IN MOLECULE C. THE 11-16 C-TERMINAL RESIDUES OF THE R2 PEPTIDE, CHAINS D, E, F BIND AT THE R2 BINDING-SITE OF THE R1 MOLECULES, CHAINS A, B, C. THE THREE N-TERMINAL RESIDUES, UNIQUE CHAIN P, ARE SITUATED BETWEEN MOL A AND C. THIS LATTER BINDING HAS NO KNOWN BIOLOGICAL RELEVANCE BUT IS ESSENTIAL FOR CRYSTAL LATTICE FORMATION. WATERS CLOSE TO SER 625 MAY REPRESENT A SULPHATE ION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 5622 5.08 %RANDOM
Rwork0.1884 ---
obs0.191 112260 99.962 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.867 Å2
Baniso -1Baniso -2Baniso -3
1-0.177 Å20.089 Å20 Å2
2--0.177 Å20 Å2
3----0.266 Å2
Refinement stepCycle: LAST / Resolution: 2.5→169.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17952 0 0 1007 18959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02218336
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.96324837
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57352246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94124.117889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.539153151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.16815120
X-RAY DIFFRACTIONr_chiral_restr0.0840.22729
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214014
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.28920
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.212564
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.21141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.561.511504
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.014218073
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.237707
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0454.56764
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 415 -
Rwork0.281 7807 -
obs--99.988 %

+
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