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- PDB-8vho: Crystal Structure of E. coli class Ia ribonucleotide reductase al... -

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Basic information

Entry
Database: PDB / ID: 8vho
TitleCrystal Structure of E. coli class Ia ribonucleotide reductase alpha subunit bound to dATP
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 / Ribonucleoside-diphosphate reductase 1 subunit alpha
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.548 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,39114
Polymers171,7542
Non-polymers2,63712
Water12,178676
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)118.513, 118.513, 290.295
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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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

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Non-polymers , 5 types, 688 molecules

#2: Chemical
ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 6.8% (w/vol) PEG3350, 80mM HEPES pH7.3, 280mM MgCl2, 4% (vol/vol) glycerol, and 1.0% CYMAL-1 detergent

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.548→50 Å / Num. obs: 68422 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 47.48 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.042 / Rrim(I) all: 0.093 / Χ2: 0.984 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.594.90.8333410.6940.4160.930.952100
2.59-2.644.90.74633880.7170.3740.8360.955100
2.64-2.694.90.64933270.7690.3260.7281.04599.9
2.69-2.754.90.50933770.8390.2560.5710.962100
2.75-2.814.90.41733620.8960.2090.4680.982100
2.81-2.874.90.33833820.9230.1690.3790.969100
2.87-2.944.90.29633560.9440.1490.3331.006100
2.94-3.024.90.24233950.9560.1220.2711.018100
3.02-3.114.90.20633690.9680.1030.2311.016100
3.11-3.214.90.16433980.980.0830.1841.027100
3.21-3.334.90.12433700.9880.0620.1391.023100
3.33-3.464.90.10333980.9910.0520.1161.089100
3.46-3.624.90.07534260.9960.0380.0840.936100
3.62-3.814.90.06334340.9970.0320.070.908100
3.81-4.054.80.05234050.9970.0260.0580.894100
4.05-4.364.80.04834660.9970.0240.0540.96100
4.36-4.84.80.05134640.9970.0260.0571.02100
4.8-5.494.70.05334800.9960.0270.060.981100
5.49-6.924.60.04235410.9980.0220.0480.99799.8
6.92-504.50.02374310.0110.0230.93999

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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: 3R1R

3r1r


Resolution: 2.548→49.785 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 3376 4.94 %
Rwork0.1647 64964 -
obs0.1667 68340 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.31 Å2 / Biso mean: 51.7427 Å2 / Biso min: 22.81 Å2
Refinement stepCycle: final / Resolution: 2.548→49.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11691 0 160 676 12527
Biso mean--67.2 57.91 -
Num. residues----1467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212133
X-RAY DIFFRACTIONf_angle_d0.6616424
X-RAY DIFFRACTIONf_chiral_restr0.0251787
X-RAY DIFFRACTIONf_plane_restr0.0022162
X-RAY DIFFRACTIONf_dihedral_angle_d12.2364556
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5484-2.58480.28871350.2692261599
2.5848-2.62340.31321390.27112697100
2.6234-2.66440.30071360.25912604100
2.6644-2.70810.27031450.25342679100
2.7081-2.75480.26141330.23352677100
2.7548-2.80490.31471450.22262659100
2.8049-2.85880.28961220.21232648100
2.8588-2.91710.25611340.21632714100
2.9171-2.98060.25421410.21532678100
2.9806-3.04990.23351370.21192690100
3.0499-3.12620.2831600.21752642100
3.1262-3.21070.28611430.20672685100
3.2107-3.30510.23561280.19572706100
3.3051-3.41180.231370.18682681100
3.4118-3.53370.20641490.1752704100
3.5337-3.67510.22171480.16122699100
3.6751-3.84230.19261330.14712705100
3.8423-4.04480.19371370.13242709100
4.0448-4.29810.1421480.12822722100
4.2981-4.62970.14651420.11972733100
4.6297-5.09520.161550.11892746100
5.0952-5.83160.16571400.13592770100
5.8316-7.34340.18791550.14552817100
7.3434-49.7850.14931340.135298499
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)
12.7542.1857-0.39093.4129-0.81212.53470.1806-0.206-0.32220.6516-0.1437-0.2891-0.0230.3075-0.06780.5090.0797-0.03450.3409-0.06310.4314-9.0352-40.50784.1627
21.1173-0.6572-0.59491.08160.66032.62130.05590.2507-0.0572-0.2309-0.1060.1513-0.08420.10760.06650.26650.0216-0.01820.3429-0.01160.2877-5.2999-41.375-36.5737
31.2069-0.207-0.4481.35820.25281.86860.04960.22070.0721-0.0985-0.05160.2205-0.2178-0.20540.01720.28110.0706-0.0260.352-0.00790.3869-17.5129-31.5465-30.0641
42.33681.35021.10062.47990.70371.7929-0.15060.4078-0.062-0.21970.20520.20950.0189-0.005-0.07750.3383-0.07670.06080.4490.01660.374919.5854-64.4249-77.7537
51.7104-0.4955-0.70540.70010.44421.4011-0.161-0.3967-0.22930.14190.06490.09810.0120.0450.07570.27290.02060.02730.42070.05940.330518.2605-60.0668-37.0657
61.599-0.0651-0.05241.14680.05811.2224-0.1108-0.255-0.3350.08470.0997-0.03680.15270.08440.0270.25880.05610.04970.34520.06930.365930.4644-69.8926-43.5914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 188 )A3 - 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 4 through 188 )B4 - 188
5X-RAY DIFFRACTION5chain 'B' and (resid 189 through 371 )B189 - 371
6X-RAY DIFFRACTION6chain 'B' and (resid 372 through 736 )B372 - 736

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