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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vhr
TitleCrystal structure of E. coli class Ia ribonucleotide reductase alpha subunit W28A variant bound to dATP and GTP
ComponentsRibonucleoside-diphosphate reductase 1 subunit alpha
KeywordsOXIDOREDUCTASE / Ribonucleotide reductase / allosteric regulation / nucleotide binding / subunit interaction
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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Ribonucleoside-diphosphate reductase 1 subunit alpha
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.55 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
C: Ribonucleoside-diphosphate reductase 1 subunit alpha
D: Ribonucleoside-diphosphate reductase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,94524
Polymers350,7284
Non-polymers6,21720
Water00
1
A: Ribonucleoside-diphosphate reductase 1 subunit alpha
B: Ribonucleoside-diphosphate reductase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,47212
Polymers175,3642
Non-polymers3,10810
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ribonucleoside-diphosphate reductase 1 subunit alpha
D: Ribonucleoside-diphosphate reductase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,47212
Polymers175,3642
Non-polymers3,10810
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.576, 141.078, 301.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

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 - 73623 - 755
2LEULEUchain BBB5 - 73624 - 755
3ASNASNchain CCC4 - 73623 - 755
4LEULEUchain DDD5 - 73624 - 755

-
Components

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


Mass: 87682.008 Da / Num. of mol.: 4 / Mutation: W28A
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
#2: Chemical
ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 6.5-7.0% (w/vol) PEG3350, 0.1M HEPES 7.0, 0.35M MgSO4, 5% (vol/vol) glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.55→50 Å / Num. obs: 57221 / % possible obs: 95.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 127.34 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.042 / Rrim(I) all: 0.078 / Χ2: 1.046 / Net I/σ(I): 8.2 / Num. measured all: 239539
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
3.55-3.6840.93854710.6480.5431.23593.6
3.68-3.824.30.62257710.710.3461.10598.10.715
3.82-44.10.4457250.650.261.26397.30.514
4-4.214.30.2257510.9610.120.88997.10.252
4.21-4.474.10.15255220.9790.0850.9593.90.175
4.47-4.824.30.10458340.9890.0570.97298.10.119
4.82-5.34.30.0858080.9930.0441.00297.70.092
5.3-6.074.10.0756010.9940.0391.00193.40.08
6.07-7.644.30.05358550.9960.0291.012970.061
7.64-504.10.03258830.9980.0181.05193.30.037

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RO9

7ro9
PDB Unreleased entry


Resolution: 3.55→49.869 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 5640 9.96 %
Rwork0.1971 50963 -
obs0.2016 56603 95.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 324.29 Å2 / Biso mean: 154.5736 Å2 / Biso min: 53.19 Å2
Refinement stepCycle: final / Resolution: 3.55→49.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23312 0 376 0 23688
Biso mean--154.76 --
Num. residues----2930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224244
X-RAY DIFFRACTIONf_angle_d0.5132882
X-RAY DIFFRACTIONf_chiral_restr0.023586
X-RAY DIFFRACTIONf_plane_restr0.0024376
X-RAY DIFFRACTIONf_dihedral_angle_d9.9419138
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A14358X-RAY DIFFRACTION5.488TORSIONAL
12B14358X-RAY DIFFRACTION5.488TORSIONAL
13C14358X-RAY DIFFRACTION5.488TORSIONAL
14D14358X-RAY DIFFRACTION5.488TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.55-3.59030.35761730.3476158591
3.5903-3.63260.38741760.3596163793
3.6326-3.67680.60421600.5481144984
3.6768-3.72340.50211910.4523170797
3.7234-3.77230.33251940.2812174098
3.7723-3.8240.27821910.2634172898
3.824-3.87860.33521900.3173171597
3.8786-3.93650.48291850.4607161991
3.9365-3.9980.29311870.2521170697
3.998-4.06350.28641850.2259172197
4.0635-4.13350.27141840.2185169197
4.1335-4.20870.27551930.2128173897
4.2087-4.28960.2331870.2057170296
4.2896-4.37710.26891780.2047167595
4.3771-4.47220.22811780.1815159391
4.4722-4.57610.22731970.1793174298
4.5761-4.69050.22011950.1777175299
4.6905-4.81720.2141930.1742172898
4.8172-4.95890.23481970.1751175598
4.9589-5.11880.23211840.1719173298
5.1188-5.30150.24942000.1725172997
5.3015-5.51350.22311920.172170596
5.5135-5.76410.22321750.1726170094
5.7641-6.06750.24381840.1836161990
6.0675-6.44690.26321980.1768174798
6.4469-6.94350.23581970.1639175397
6.9435-7.640.21241920.1657175396
7.64-8.74040.19341810.1531166290
8.7404-10.99250.14841980.1243175696
10.9925-49.8690.2142050.1841182494
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)
10.7050.29050.43291.24310.39331.27270.13420.4315-0.1969-0.53660.1178-0.16940.18380.030100.84240.2478-0.09370.99490.01160.9049-21.518219.9476-175.0149
20.7037-0.0905-0.17431.58280.44460.1554-0.1484-0.28930.07950.561-0.0533-0.1773-0.01140.0531-00.5244-0.0072-0.06430.8364-0.02230.8526-28.685521.6098-135.4171
31.21710.3082-0.3031.6674-0.10892.08760.2036-0.1106-0.052-0.0125-0.1497-0.1660.12590.197700.60160.0939-0.07841.02910.08190.9907-8.545527.209-141.424
41.6045-0.89751.59130.5045-0.79821.76530.195-0.02170.0325-0.17810.18980.30210.5451-0.4843-01.2494-0.1160.08461.22170.07131.0086-46.65999.4203-91.2522
50.21170.29340.02341.6337-0.44210.19810.34790.1350.1725-0.4881-0.0130.09380.61220.0960.00090.8021-0.1276-0.10591.22330.01861.1249-41.958115.0147-131.1692
61.18730.7117-0.58861.67890.16491.65370.31080.3914-0.5315-0.2368-0.215-0.35550.9045-0.081101.12160.0095-0.24711.25840.0991.3113-52.18930.5711-142.1678
70.7568-0.31440.49840.1263-0.18031.44280.1727-0.1982-0.0775-0.25610.11280.29860.4634-0.552200.9505-0.2877-0.06541.0050.18881.0562-61.79433.7998-118.3035
80.86590.8718-0.35060.8347-0.47241.89360.1411-0.35670.12270.5032-0.0304-0.0177-0.720.2029-01.3686-0.0372-0.0351.1049-0.04731.0318-21.834520.2675-18.7775
90.7743-0.73640.85630.9862-0.26421.75250.12930.2294-0.3395-0.3601-0.03130.1843-0.96470.7150.00731.1544-0.07630.03950.82090.14931.2656-25.223720.0635-62.1812
100.9289-0.8395-1.00120.74950.95291.3036-0.2770.16140.3475-0.02640.367-0.06-1.34560.58880.00032.0183-0.061-0.08161.14450.13931.6986-24.470332.0912-53.8321
110.17870.0926-0.46790.2262-0.78552.83060.4256-0.07780.84120.85910.2788-0.1478-2.1829-0.22850.2272.180.50840.34951.10230.19311.848-31.907535.7773-40.9551
120.4957-0.0463-0.04820.1257-0.22880.4460.75791.5959-0.4083-0.98050.2860.57710.27270.03370.00111.85610.1548-0.16891.6330.00611.5315-21.9702-9.249-106.3914
130.05310.23760.08481.03480.24170.97460.65180.9181-0.0254-0.2132-0.0821-0.20710.14390.2759-01.43340.1031-0.01531.7959-0.16231.28980.1244-0.7279-93.3978
140.6515-0.1075-1.38010.49350.59273.18110.5095-0.70960.37290.6345-0.0778-0.64910.77952.25480.13741.10130.1515-0.16791.26910.1041.0837-8.28463.9328-57.8218
151.0062-0.3057-1.09860.66430.04481.34790.60010.3179-0.3404-0.59060.03670.42581.71380.77210.00331.57570.4782-0.47961.5289-0.00911.5121-8.6256-13.8236-46.726
160.74311.16560.32641.82580.6211.89280.17480.2721-0.4767-0.9444-0.1192-0.2871.3670.8692-01.90320.6258-0.2162.0414-0.17291.64398.6991-13.2442-69.49
173.4001-0.26170.41520.0192-0.02720.0481-0.02591.1651-0.30960.70440.1947-0.5511.35350.4070.16991.85650.3384-0.40171.2107-0.32981.3773-13.6288-21.7827-82.6939
181.1912-0.49010.58290.5607-0.21870.9360.73670.65650.1984-0.4448-0.1806-0.95290.69390.5480.00052.0610.4035-0.22760.7913-0.15011.1826-9.6776-24.9027-63.0114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 212 )A4 - 212
2X-RAY DIFFRACTION2chain 'A' and (resid 213 through 301 )A213 - 301
3X-RAY DIFFRACTION3chain 'A' and (resid 302 through 736 )A302 - 736
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 212 )B5 - 212
5X-RAY DIFFRACTION5chain 'B' and (resid 213 through 301 )B213 - 301
6X-RAY DIFFRACTION6chain 'B' and (resid 302 through 422 )B302 - 422
7X-RAY DIFFRACTION7chain 'B' and (resid 423 through 736 )B423 - 736
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 248 )C4 - 248
9X-RAY DIFFRACTION9chain 'C' and (resid 249 through 371 )C249 - 371
10X-RAY DIFFRACTION10chain 'C' and (resid 372 through 493 )C372 - 493
11X-RAY DIFFRACTION11chain 'C' and (resid 494 through 736 )C494 - 736
12X-RAY DIFFRACTION12chain 'D' and (resid 5 through 74 )D5 - 74
13X-RAY DIFFRACTION13chain 'D' and (resid 75 through 212 )D75 - 212
14X-RAY DIFFRACTION14chain 'D' and (resid 213 through 301 )D213 - 301
15X-RAY DIFFRACTION15chain 'D' and (resid 302 through 422 )D302 - 422
16X-RAY DIFFRACTION16chain 'D' and (resid 423 through 624 )D423 - 624
17X-RAY DIFFRACTION17chain 'D' and (resid 625 through 675 )D625 - 675
18X-RAY DIFFRACTION18chain 'D' and (resid 676 through 736 )D676 - 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