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- PDB-7b9p: Structure of Ribonucleotide reductase from Rhodobacter sphaeroides -

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Basic information

Entry
Database: PDB / ID: 7b9p
TitleStructure of Ribonucleotide reductase from Rhodobacter sphaeroides
ComponentsVitamin B12-dependent ribonucleotide reductase
KeywordsOXIDOREDUCTASE / Ribonucleotide Reductase / Thiyl Radical Enzyme / Allosteric Effector
Function / homology
Function and homology information


cobalamin binding / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / cobalt ion binding / DNA biosynthetic process / DNA replication / nucleotide binding
Similarity search - Function
Ribonucleotide reductase class II vitamin B12-dependent, N-terminal domain / Class II vitamin B12-dependent ribonucleotide reductase / YebC-like / Ribonucleotide reductase, adenosylcobalamin-dependent / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Vitamin B12-dependent ribonucleotide reductase
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.646 Å
AuthorsWilk, P. / Feiler, C. / Loderer, C. / Kabinger, F.
CitationJournal: Biochemistry / Year: 2022
Title: HUG Domain Is Responsible for Active Dimer Stabilization in an NrdJd Ribonucleotide Reductase.
Authors: Fietze, T. / Wilk, P. / Kabinger, F. / Anoosheh, S. / Hofer, A. / Lundin, D. / Feiler, C.G. / Weiss, M.S. / Loderer, C.
History
DepositionDec 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 10, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitamin B12-dependent ribonucleotide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0383
Polymers100,5221
Non-polymers5152
Water2,468137
1
A: Vitamin B12-dependent ribonucleotide reductase
hetero molecules

A: Vitamin B12-dependent ribonucleotide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,0766
Polymers201,0452
Non-polymers1,0314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_667-y+1,-x+1,-z+13/61
Buried area8250 Å2
ΔGint-46 kcal/mol
Surface area68090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.748, 140.748, 364.277
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Vitamin B12-dependent ribonucleotide reductase


Mass: 100522.297 Da / Num. of mol.: 1 / Mutation: V926Stop
Source method: isolated from a genetically manipulated source
Details: From the full length protein with 1218 aa, the C-terminal CRD domain was deleted by insertion of a stop codon at postion 926.
Source: (gene. exp.) Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: nrd, RSP_2495 / Plasmid: pET28b(+) / Details (production host): N-Terminal His-Tag fusion / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q3J3H6, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 5.18 Å3/Da / Density % sol: 76.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Precipitant: 30% PEG 1500, 20% Glycerol Protein solution: 45 mg/mL Protein + 100 uM dATP Hanging drop experiment: 1.0 uL Protein solution + 1.0 uL Precipitant over 500 uL precipitant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.646→47.86 Å / Num. obs: 62949 / % possible obs: 99.83 % / Redundancy: 19.29 % / CC1/2: 0.999 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.04 / Rrim(I) all: 0.174 / Net I/σ(I): 13.9
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 19.7 % / Rmerge(I) obs: 7.684 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 6078 / CC1/2: 0.148 / Rpim(I) all: 1.756 / Rrim(I) all: 7.886 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ensemble

Resolution: 2.646→47.86 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2718 2098 3.34 %
Rwork0.2298 60787 -
obs0.2312 62885 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 230 Å2 / Biso mean: 114.4113 Å2 / Biso min: 58.67 Å2
Refinement stepCycle: final / Resolution: 2.646→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6888 0 31 137 7056
Biso mean--111.12 101.59 -
Num. residues----899
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6462-2.70780.46721330.4381385796
2.7078-2.77550.40391370.43963100
2.7755-2.85050.38891360.37713980100
2.8505-2.93440.34361390.33214017100
2.9344-3.02910.36261370.30863976100
3.0291-3.13730.37561390.30114008100
3.1373-3.26290.35651380.28584013100
3.2629-3.41140.28711380.26584007100
3.4114-3.59120.31771400.23964044100
3.5912-3.81610.25791390.20794036100
3.8161-4.11060.24321410.19534062100
4.1106-4.52390.24431410.17514090100
4.5239-5.17790.21311420.19214115100
5.1779-6.5210.2661440.23594187100
6.521-47.860.26091540.2264432100
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)
1-0.0195-0.05260.4240.1117-0.32450.64710.17930.2617-0.062-0.08350.23170.54040.1716-0.68580.0010.7747-0.0813-0.06241.19640.15211.084914.344152.4251363.3871
22.0792-0.7725-0.01470.7704-0.33321.20750.12220.5056-0.0097-0.0579-0.2805-0.2530.09020.5344-0.01070.70990.14890.10391.14440.04050.771250.883154.2611366.9506
31.20160.0025-0.13711.7810.67792.00330.0104-0.0398-0.1375-0.33910.008-0.0899-0.2663-0.40160.00030.60930.1250.0170.88040.13620.707820.531263.7635394.3827
42.0852-0.63860.45910.94920.22290.46130.12440.6415-0.4332-0.3530.00080.04740.57130.26450.00020.89160.0648-0.00370.9894-0.13450.862632.376841.8165362.2143
52.7120.71330.82881.9197-0.70641.0281-0.3012-0.12460.48040.81960.1799-0.5633-0.41520.58580.29290.8957-0.2981-0.11911.46870.21621.00728.042285.6743348.1618
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 814 through 920 )A814 - 920
2X-RAY DIFFRACTION2chain 'A' and (resid 2 through 244 )A2 - 244
3X-RAY DIFFRACTION3chain 'A' and (resid 245 through 446 )A245 - 446
4X-RAY DIFFRACTION4chain 'A' and (resid 447 through 747 )A447 - 747
5X-RAY DIFFRACTION5chain 'A' and (resid 748 through 813 )A748 - 813

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