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- PDB-8vhq: Crystal structure of E. coli class Ia ribonucleotide reductase al... -

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Basic information

Entry
Database: PDB / ID: 8vhq
TitleCrystal structure of E. coli class Ia ribonucleotide reductase alpha subunit W28A variant bound to dATP and ATP
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
ADENOSINE-5'-TRIPHOSPHATE / 2'-DEOXYADENOSINE 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: 3.4 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)356,88124
Polymers350,7284
Non-polymers6,15320
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)178,44012
Polymers175,3642
Non-polymers3,07610
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)178,44012
Polymers175,3642
Non-polymers3,07610
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.695, 139.929, 300.766
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
2GLNGLNchain BBB3 - 73622 - 755
3ASNASNchain CCC4 - 73623 - 755
4ASNASNchain DDD4 - 73623 - 755

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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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.61 %
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.

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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: 3.4→50 Å / Num. obs: 65872 / % possible obs: 98.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 111.95 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.054 / Rrim(I) all: 0.109 / Χ2: 1.106 / Net I/σ(I): 5.4 / Num. measured all: 249742
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.523.60.79263660.540.470.9261.16797.1
3.52-3.663.90.53865250.7650.3060.6221.11299.3
3.66-3.833.90.35865620.8770.2050.4151.19499.5
3.83-4.033.90.23765860.9350.1370.2751.17999.6
4.03-4.283.80.16265710.9670.0950.1881.199.7
4.28-4.613.60.11765140.980.070.1371.14698.1
4.61-5.083.90.0966300.9880.0520.1051.10599.9
5.08-5.813.90.08267000.9910.0480.0951.06699.9
5.81-7.323.70.06566550.9910.0380.0760.97898.6
7.32-503.80.04367630.9970.0250.051.01896.1

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Phasing

PhasingMethod: molecular replacement

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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: 3.4→49.618 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 3272 5 %
Rwork0.2043 62129 -
obs0.2057 65401 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 225.19 Å2 / Biso mean: 124.9191 Å2 / Biso min: 54.98 Å2
Refinement stepCycle: final / Resolution: 3.4→49.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23333 0 372 0 23705
Biso mean--106.13 --
Num. residues----2933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224261
X-RAY DIFFRACTIONf_angle_d0.50532903
X-RAY DIFFRACTIONf_chiral_restr0.023589
X-RAY DIFFRACTIONf_plane_restr0.0024377
X-RAY DIFFRACTIONf_dihedral_angle_d8.7869145
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A14337X-RAY DIFFRACTION3.956TORSIONAL
12B14337X-RAY DIFFRACTION3.956TORSIONAL
13C14337X-RAY DIFFRACTION3.956TORSIONAL
14D14337X-RAY DIFFRACTION3.956TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4-3.45080.36581330.3419260096
3.4508-3.50470.31191390.3112261897
3.5047-3.56210.32571420.29132664100
3.5621-3.62350.33481390.2881268299
3.6235-3.68940.3251440.2719270599
3.6894-3.76040.25111410.25752686100
3.7604-3.83710.271480.23942667100
3.8371-3.92050.26891390.23032707100
3.9205-4.01160.25371400.22592729100
4.0116-4.11190.24791410.21522684100
4.1119-4.2230.25511420.21372703100
4.223-4.34720.24991430.21262707100
4.3472-4.48750.19911470.1978272199
4.4875-4.64770.22811320.1923259896
4.6477-4.83370.2111430.19862742100
4.8337-5.05350.21721410.18572698100
5.0535-5.31960.20391470.19692759100
5.3196-5.65250.22361440.20022756100
5.6525-6.08820.25491440.19892730100
6.0882-6.69950.20711470.2034273898
6.6995-7.66590.22521440.186271798
7.6659-9.64660.20121470.1617279099
9.6466-49.6180.19961450.1691272892
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)
11.19040.21110.14553.78321.40781.92910.1044-0.28620.24540.4921-0.05670.2178-0.3548-0.02501.2639-0.16520.10571.36790.00231.078735.1274-15.561326.2515
21.137-0.38210.40721.3429-0.58862.79660.16620.16670.0922-0.1474-0.1405-0.035-0.09240.082400.7848-0.07940.07981.0555-0.00061.006939.4026-26.4413-11.6318
31.4708-0.04220.06572.27380.10432.13880.1394-0.08830.23240.1024-0.0395-0.3447-0.24640.302500.7882-0.10690.04411.17540.02191.072253.2472-27.4899-2.5635
42.35181.0533-1.58591.6519-0.79042.74410.18250.37350.0922-0.18330.0939-0.1024-0.3329-0.185401.41180.2279-0.0491.33110.06651.10510.2854-8.9919-59.6373
51.1483-0.23020.50041.71720.64570.83480.24370.22830.1341-0.12740.01820.1161-0.51510.1433-00.8673-0.0110.04391.10490.02941.064815.0748-14.8034-19.6299
61.42980.01450.17341.074-0.04652.81570.25260.14110.2558-0.1456-0.030.0616-0.6356-0.234201.11970.20570.11771.11520.07361.1583-1.9107-2.6673-25.4869
71.2729-1.408602.66971.76922.81740.39960.46820.3177-0.8432-0.0135-0.109-0.951-0.047502.21220.04810.19171.52680.17641.529423.414320.065214.3125
81.85750.65150.72612.11880.11555.13060.0324-0.10550.1347-0.30160.2825-0.3161-1.2528-0.048501.49930.07980.14671.0239-0.16051.569423.182825.083356.4415
90.01750.1662-0.07462.03230.52023.65920.24620.10770.6707-0.72050.2753-0.5182-1.52290.7727-02.1621-0.37120.36681.308-0.14531.942731.781535.522540.9355
101.94840.59010.1750.8270.83381.47040.5792-0.4331-0.07210.1117-0.21080.11740.6148-0.95401.8772-0.1184-0.04442.1530.11751.550211.0248-3.623999.77
111.64390.3333-0.61061.5328-0.43092.07630.1364-0.2727-0.0857-0.04040.28440.12730.6951-0.4596-01.4652-0.3002-0.2231.53650.11471.5715.3397-3.583160.6749
121.9240.3324-0.26751.0233-0.17582.2550.0056-0.1047-0.30630.03260.17340.23921.0026-0.613202.0822-0.4995-0.25271.58370.11991.71140.0112-17.012766.0503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 168 )A4 - 168
2X-RAY DIFFRACTION2chain 'A' and (resid 169 through 536 )A169 - 536
3X-RAY DIFFRACTION3chain 'A' and (resid 537 through 736 )A537 - 736
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 212 )B3 - 212
5X-RAY DIFFRACTION5chain 'B' and (resid 213 through 301 )B213 - 301
6X-RAY DIFFRACTION6chain 'B' and (resid 302 through 736 )B302 - 736
7X-RAY DIFFRACTION7chain 'C' and (resid 4 through 212 )C4 - 212
8X-RAY DIFFRACTION8chain 'C' and (resid 213 through 493 )C213 - 493
9X-RAY DIFFRACTION9chain 'C' and (resid 494 through 736 )C494 - 736
10X-RAY DIFFRACTION10chain 'D' and (resid 4 through 168 )D4 - 168
11X-RAY DIFFRACTION11chain 'D' and (resid 169 through 371 )D169 - 371
12X-RAY DIFFRACTION12chain 'D' and (resid 372 through 736 )D372 - 736

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