[English] 日本語
Yorodumi
- PDB-5r1r: RIBONUCLEOTIDE REDUCTASE E441A MUTANT R1 PROTEIN FROM ESCHERICHIA COLI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5r1r
TitleRIBONUCLEOTIDE REDUCTASE E441A MUTANT R1 PROTEIN FROM ESCHERICHIA COLI
Components
  • RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
  • RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
KeywordsCOMPLEX (OXIDOREDUCTASE/PEPTIDE) / RIBONUCLEOTIDE REDUCTASE / DEOXYRIBONUCLEOTIDE SYNTHESIS / RADICAL CHEMISTRY / ALLOSTERIC REGULATION / SPECIFICITY / COMPLEX (OXIDOREDUCTASE-PEPTIDE) / COMPLEX (OXIDOREDUCTASE-PEPTIDE) complex
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 / RIGID BODY / Resolution: 3.1 Å
AuthorsEriksson, M. / Eklund, H.
Citation
Journal: J.Biol.Chem. / Year: 1997
Title: A new mechanism-based radical intermediate in a mutant R1 protein affecting the catalytically essential Glu441 in Escherichia coli ribonucleotide reductase.
Authors: Persson, A.L. / Eriksson, M. / Katterle, B. / Potsch, S. / Sahlin, M. / Sjoberg, B.M.
#1: 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.
#2: Journal: Nature / Year: 1994
Title: Structure of Ribonucleotide Reductase Protein R1
Authors: Uhlin, U. / Eklund, H.
History
DepositionSep 17, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
P: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)266,5437
Polymers266,5437
Non-polymers00
Water1,62190
1
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
P: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)90,3623
Polymers90,3623
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)88,0902
Polymers88,0902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-14 kcal/mol
Surface area28750 Å2
MethodPISA
3
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)88,0902
Polymers88,0902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-14 kcal/mol
Surface area28720 Å2
MethodPISA
4
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)528,54312
Polymers528,54312
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area28860 Å2
ΔGint-177 kcal/mol
Surface area154580 Å2
MethodPISA
5
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
x 6


Theoretical massNumber of molelcules
Total (without water)528,54312
Polymers528,54312
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area28740 Å2
ΔGint-177 kcal/mol
Surface area154600 Å2
MethodPISA
6
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)264,2716
Polymers264,2716
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area10730 Å2
ΔGint-74 kcal/mol
Surface area81000 Å2
MethodPISA
7
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)264,2716
Polymers264,2716
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area10630 Å2
ΔGint-72 kcal/mol
Surface area81080 Å2
MethodPISA
8
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)264,2716
Polymers264,2716
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10590 Å2
ΔGint-73 kcal/mol
Surface area81070 Å2
MethodPISA
9
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)514,9146
Polymers514,9146
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area15200 Å2
ΔGint-87 kcal/mol
Surface area154580 Å2
MethodPISA
10
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)176,1814
Polymers176,1814
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-39 kcal/mol
Surface area55010 Å2
MethodPISA
11
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)176,1814
Polymers176,1814
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area6150 Å2
ΔGint-39 kcal/mol
Surface area54960 Å2
MethodPISA
12
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)88,0902
Polymers88,0902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-14 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.810, 223.810, 334.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.902159, 0.431394, 0.002933), (0.431403, 0.902141, 0.005709), (-0.000183, 0.006416, -0.999979)-55.9091, 12.4334, -6.602
2given(-0.731638, 0.681681, -0.004058), (-0.681662, -0.731648, -0.005263), (-0.006557, -0.001084, 0.999978)-88.0775, 94.5832, 3.0105

-
Components

#1: Protein RIBONUCLEOTIDE REDUCTASE R1 PROTEIN


Mass: 85819.055 Da / Num. of mol.: 3 / Mutation: E441A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NRDA / Production host: Escherichia coli (E. coli)
References: UniProt: P00452, ribonucleoside-diphosphate reductase
#2: Protein/peptide
RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Mass: 2271.392 Da / Num. of mol.: 4 / Fragment: C-TERMINAL PORTION, 20 RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P69924
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 3.02 Å3/Da / Density % sol: 56 %
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLIZED FROM 1.7 M LITHIUM SULFATE, AND 10 MM MAGNESIUM SULFATE IN 25 MM CITRATE BUFFER AT PH 6.0 THE PROTEIN SOLUTION CONTAINED 17 MG/ML R1 PROTEIN, 20 FOLD EXCESS OF A 20- ...Details: PROTEIN WAS CRYSTALLIZED FROM 1.7 M LITHIUM SULFATE, AND 10 MM MAGNESIUM SULFATE IN 25 MM CITRATE BUFFER AT PH 6.0 THE PROTEIN SOLUTION CONTAINED 17 MG/ML R1 PROTEIN, 20 FOLD EXCESS OF A 20-RESIDUE PEPTIDE CORRESPONDING TO THE C-TERMINUS OF THE R2 SUBUNIT AND IS ESSENTIAL FOR CRYSTALLIZATION
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 mg/mlprotein1drop
217 %lithium sulfate1reservoir
310 mMmagnesium sulfate1reservoir
425 mMcitrate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Type: NSLS / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 53031 / % possible obs: 90.9 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 13.2
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.29 / % possible all: 89.9

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
REFMACrefinement
TNTphasing
RefinementMethod to determine structure: RIGID BODY
Starting model: PDB ENTRY 1RLR

1rlr


Resolution: 3.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 -2 %RANDOM
Rwork0.196 ---
obs0.199 52838 90.9 %-
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18533 0 0 90 18623
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 52838
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d2.4

+
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