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- PDB-7b9q: The SERp optimized structure of Ribonucleotide reductase from Rho... -

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Basic information

Entry
Database: PDB / ID: 7b9q
TitleThe SERp optimized structure of Ribonucleotide reductase from Rhodobacter sphaeroides
ComponentsVitamin B12-dependent ribonucleotide reductase
KeywordsOXIDOREDUCTASE / Ribonucleotide Reductase / Thiyl Radical Enzyme / Allosteric Effector
Function / homology2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / :
Function and homology information
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsLoderer, C. / Feiler, C. / Wilk, P. / 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 1.3Jan 31, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)201,7276
Polymers200,6962
Non-polymers1,0314
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-50 kcal/mol
Surface area65640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.588, 161.588, 97.308
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Vitamin B12-dependent ribonucleotide reductase


Mass: 100348.188 Da / Num. of mol.: 2 / Mutation: V926Stop, E96A, E97A, E98A
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. In order to reduce the surface entropy, the three glutamic acids ...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. In order to reduce the surface entropy, the three glutamic acids on the positions 96, 97 and 98 were exchanged to alanine.
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: HGN32_08220 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A6H2IRA4, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H16N5O12P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Precipitant: 40% MPD, 5% PEG 8000, 100 mM MES-Bufffer Protein sample: 25 mg/mL Enzyme + 100 uM dATP Ratio 1:1

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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: 2.776→46.588 Å / Num. obs: 63329 / % possible obs: 99.8 % / Redundancy: 7.641 % / Biso Wilson estimate: 71.558 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.197 / Rrim(I) all: 0.212 / Χ2: 1.009 / Net I/σ(I): 9.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.78-2.947.4082.5090.777448810167100550.2932.69598.9
2.94-3.157.9311.3561.5575984958395810.5731.449100
3.15-3.47.6840.732.8968264888988840.8170.78399.9
3.4-3.727.5110.3565.761991825482530.9510.382100
3.72-4.167.8820.19810.258765745874560.9850.211100
4.16-4.797.4390.12315.6649008658965880.9940.133100
4.79-5.867.9380.10818.0344487560556040.9960.116100
5.86-8.227.4180.07125.1132512438543830.9980.076100
8.22-46.5887.2810.03349.2218384254125250.9990.03599.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B9P

7b9p


Resolution: 2.78→46.588 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2707 2100 3.32 %
Rwork0.2203 61220 -
obs0.222 63320 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 229.08 Å2 / Biso mean: 94.5947 Å2 / Biso min: 26.74 Å2
Refinement stepCycle: final / Resolution: 2.78→46.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13183 0 62 209 13454
Biso mean--74.4 69.99 -
Num. residues----1728
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.78-2.84080.46751340.3855391497
2.8408-2.91180.38011390.34414055100
2.9118-2.99060.38321400.29944099100
2.9906-3.07850.30551390.26424041100
3.0785-3.17790.3051400.25274082100
3.1779-3.29140.25191390.23634056100
3.2914-3.42320.26791400.23094090100
3.4232-3.57890.26931400.20394069100
3.5789-3.76750.27321410.19814126100
3.7675-4.00350.25851390.18764049100
4.0035-4.31240.24631410.17464098100
4.3124-4.7460.22831400.17824097100
4.746-5.43180.25231420.19854115100
5.4318-6.840.28351410.24794120100
6.84-46.5880.26221450.22984209100
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)
10.5009-0.243-0.12510.58740.3020.31680.0401-0.0873-0.09080.1198-0.10090.0428-0.0438-0.07-00.3913-0.06160.06760.4588-0.030.2193-3.404-26.60415.559
20.34470.03760.10860.42410.40450.33710.19730.1629-0.56490.0106-0.20970.16940.1806-0.1552-0.11110.57960.05420.01310.5109-0.11630.6402-8.6908-65.4848-9.9769
30.59820.0856-0.05690.94460.23740.26920.0532-0.0371-0.15640.07210.0139-0.40460.12210.18520.02490.3610.00340.02960.42840.01750.328617.0278-40.73930.4313
40.0684-0.016-0.06660.07840.04060.08440.0257-0.4487-0.00970.432-0.07180.41560.3322-0.03470.1351.3125-0.35630.85380.9552-0.03940.9795-40.6362-73.503825.2139
50.1854-0.1411-0.04080.2580.13160.07880.0504-0.0851-0.03030.3035-0.28210.36740.1748-0.2248-0.00020.5256-0.0660.09770.5149-0.14260.6751-26.7222-53.34921.9449
60.33160.33550.21050.54550.51490.4326-0.01970.3137-0.447-0.1113-0.09490.32610.05650.05020.00110.53690.13130.02860.5554-0.18380.6365-9.7535-65.2269-17.5771
7-0.0334-0.016-0.22970.2317-0.01270.4875-0.04590.01830.20630.2122-0.63951.46810.1267-0.4503-1.8510.5826-0.10680.42430.812-0.64781.565-48.055-71.0416-2.83
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 244 )A1 - 244
2X-RAY DIFFRACTION2chain 'A' and (resid 245 through 447 )A245 - 447
3X-RAY DIFFRACTION3chain 'A' and (resid 448 through 920 )A448 - 920
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 186 )B2 - 186
5X-RAY DIFFRACTION5chain 'B' and (resid 187 through 295 )B187 - 295
6X-RAY DIFFRACTION6chain 'B' and (resid 296 through 426 )B296 - 426
7X-RAY DIFFRACTION7chain 'B' and (resid 427 through 919 )B427 - 919

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