[English] 日本語
Yorodumi
- PDB-8vhn: Crystal Structure of E. coli class Ia ribonucleotide reductase al... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vhn
TitleCrystal Structure of E. coli class Ia ribonucleotide reductase alpha subunit bound to two ATP molecules
ComponentsRibonucleoside-diphosphate reductase 1 subunit alpha
KeywordsOXIDOREDUCTASE / Ribonucleotide reductase / allosteric regulation / nucleotide binding / subunit
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 / ATP binding / identical protein binding / cytosol
Similarity search - Function
ATP-cone domain / ATP cone domain / ATP-cone domain profile. / 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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Ribonucleoside-diphosphate reductase 1 subunit alpha
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsFunk, M.A. / Zimanyi, C.M. / Drennan, C.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM08334 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-ES002109 United States
National Science Foundation (NSF, United States)0645960 United States
CitationJournal: Biochemistry / Year: 2024
Title: How ATP and dATP Act as Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase.
Authors: Funk, M.A. / Zimanyi, C.M. / Andree, G.A. / Hamilos, A.E. / Drennan, C.L.
History
DepositionJan 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,46916
Polymers171,7542
Non-polymers3,71514
Water13,655758
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.991, 118.991, 290.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ASP / End label comp-ID: ASP

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASNASNchain AAA4 - 7364 - 736
2LEULEUchain BBB5 - 7365 - 736

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Ribonucleoside-diphosphate reductase 1 subunit alpha / Protein B1 / Ribonucleoside-diphosphate reductase 1 R1 subunit / Ribonucleotide reductase 1


Mass: 85877.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: nrdA, dnaF, b2234, JW2228 / Production host: Escherichia coli (E. coli)
References: UniProt: P00452, ribonucleoside-diphosphate reductase

-
Non-polymers , 5 types, 772 molecules

#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 8.0% (w/vol)PEG3350, 80 mM HEPES pH 7.3, 280 mM magnesium chloride, 4% (vol/vol) glycerol, 1.0% CYMAL-1 detergent

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97936 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2.62→50 Å / Num. obs: 63413 / % possible obs: 99.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 44.68 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.041 / Rrim(I) all: 0.115 / Χ2: 1.024 / Net I/σ(I): 8.1 / Num. measured all: 458752
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.62-2.677.10.77231460.7560.30.8310.90599.5
2.67-2.717.30.64931310.830.2480.6970.90399.9
2.71-2.777.30.54431180.8740.2070.5840.936100
2.77-2.827.40.44331260.9190.1680.4750.967100
2.82-2.887.30.37531240.9310.1420.4020.989100
2.88-2.957.40.33531470.9430.1280.3591.01999.9
2.95-3.027.40.28531290.9610.1080.3061.05299.6
3.02-3.117.40.25131400.9660.0960.271.08499.6
3.11-3.27.30.20331340.9770.0770.2181.05999.6
3.2-3.37.30.16931670.9830.0640.1821.08799.6
3.3-3.427.30.14431300.9870.0550.1551.1299.6
3.42-3.567.30.11431480.9920.0430.1231.07799.5
3.56-3.727.20.09831780.9940.0370.1051.06899.7
3.72-3.917.30.08131700.9960.0310.0871.05399.8
3.91-4.167.20.07331760.9960.0280.0781.01199.6
4.16-4.487.20.06731880.9970.0250.0720.99599.3
4.48-4.937.20.06332010.9970.0240.0680.97499.3
4.93-5.647.10.06732360.9960.0260.0721.199.2
5.64-7.116.90.0632500.9970.0230.0651.03598.5
7.11-506.70.04833740.9980.0180.0521.03495.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RO8

7ro8
PDB Unreleased entry


Resolution: 2.62→47.852 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2086 3103 4.9 %
Rwork0.166 60245 -
obs0.1681 63348 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 215.5 Å2 / Biso mean: 47.6696 Å2 / Biso min: 1.17 Å2
Refinement stepCycle: final / Resolution: 2.62→47.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11674 0 226 758 12658
Biso mean--67.58 51.01 -
Num. residues----1465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712186
X-RAY DIFFRACTIONf_angle_d0.85316513
X-RAY DIFFRACTIONf_chiral_restr0.041797
X-RAY DIFFRACTIONf_plane_restr0.0042188
X-RAY DIFFRACTIONf_dihedral_angle_d12.2964595
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7054X-RAY DIFFRACTION4.422TORSIONAL
12B7054X-RAY DIFFRACTION4.422TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.62-2.66070.3071400.2732270499
2.6607-2.70440.28741260.25872720100
2.7044-2.7510.25711250.24032699100
2.751-2.8010.30851450.22352717100
2.801-2.85490.28881230.21832728100
2.8549-2.91310.26871330.22242715100
2.9131-2.97650.25321450.21852696100
2.9765-3.04570.25611470.2132706100
3.0457-3.12190.26811460.222697100
3.1219-3.20630.29151540.2092702100
3.2063-3.30060.25381300.18852741100
3.3006-3.40710.24571360.18162705100
3.4071-3.52880.20871450.17622713100
3.5288-3.67010.20621480.16622720100
3.6701-3.8370.19881450.14962775100
3.837-4.03920.16251420.13112726100
4.0392-4.29210.15391470.12582744100
4.2921-4.62330.1721360.1272276299
4.6233-5.08810.16491580.1294275999
5.0881-5.82320.18161440.1433279999
5.8232-7.33240.20941540.1513280799
7.3324-47.8520.15851340.1398291096
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9262.1899-1.10162.7554-0.882.07370.096-0.1974-0.28350.4358-0.0861-0.24690.00940.3154-0.01340.5190.0898-0.04840.4143-0.05170.4886-8.6539-40.36564.1914
21.0414-0.5704-0.57381.03420.62082.0280.03320.248-0.0164-0.2042-0.07380.1041-0.01010.08120.02450.38740.0211-0.00190.4807-0.00940.3892-5.1093-41.2454-36.558
31.2944-0.2788-0.47671.07690.2521.69460.06010.25130.0851-0.1226-0.04380.1365-0.2521-0.1726-0.01040.39710.0735-0.01750.4390.0030.441-17.3059-31.4597-29.9932
42.15981.71181.17323.07920.83821.4331-0.25860.44260.0056-0.42540.33850.3085-0.01870.0241-0.08810.4739-0.12190.02250.60270.03920.448319.529-64.2412-77.7366
51.4143-0.1969-0.78270.74230.05932.1454-0.1389-0.3178-0.16690.17180.07230.06670.0106-0.03040.05720.36840.00670.02020.49320.03080.423919.2623-60.6175-34.5154
61.61230.1138-0.20131.86270.0851.0934-0.0523-0.1577-0.13930.10790.1063-0.11210.00670.1023-0.06210.32190.01160.00660.41550.0070.388134.6926-65.1051-44.2198
72.21730.40.94961.16440.47543.492-0.01430.0707-0.56970.00280.11240.19850.3188-0.2411-0.08810.3987-0.00210.04060.40190.03260.647522.5741-80.8661-48.5281
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 188 )A4 - 188
2X-RAY DIFFRACTION2chain 'A' and (resid 189 through 371 )A189 - 371
3X-RAY DIFFRACTION3chain 'A' and (resid 372 through 736 )A372 - 736
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 188 )B5 - 188
5X-RAY DIFFRACTION5chain 'B' and (resid 189 through 390 )B189 - 390
6X-RAY DIFFRACTION6chain 'B' and (resid 391 through 622 )B391 - 622
7X-RAY DIFFRACTION7chain 'B' and (resid 623 through 736 )B623 - 736

+
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