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- PDB-7aik: Ribonucleotide Reductase R2 protein from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 7aik
TitleRibonucleotide Reductase R2 protein from Aquifex aeolicus
ComponentsRibonucleoside-diphosphate reductase subunit beta,Ribonucleoside-diphosphate reductase subunit betaRibonucleotide reductase
KeywordsOXIDOREDUCTASE / allosteric regulation
Function / homology
Function and homology information


intron homing / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / intein-mediated protein splicing / deoxyribonucleotide biosynthetic process / endonuclease activity / DNA replication / metal ion binding
Similarity search - Function
Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Intein N-terminal splicing region ...Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / Ribonucleoside-diphosphate reductase subunit beta
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRehling, D. / Scaletti, E.R. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-03406 Sweden
CitationJournal: Biochemistry / Year: 2022
Title: Structural and Biochemical Investigation of Class I Ribonucleotide Reductase from the Hyperthermophile Aquifex aeolicus.
Authors: Rehling, D. / Scaletti, E.R. / Rozman Grinberg, I. / Lundin, D. / Sahlin, M. / Hofer, A. / Sjoberg, B.M. / Stenmark, P.
History
DepositionSep 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Data collection / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / diffrn_source / refine
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _refine.pdbx_diffrn_id
Revision 1.2Jan 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

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase subunit beta,Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7313
Polymers38,6191
Non-polymers1122
Water2,000111
1
A: Ribonucleoside-diphosphate reductase subunit beta,Ribonucleoside-diphosphate reductase subunit beta
hetero molecules

A: Ribonucleoside-diphosphate reductase subunit beta,Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4616
Polymers77,2382
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area6050 Å2
ΔGint-65 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.420, 69.420, 177.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ribonucleoside-diphosphate reductase subunit beta,Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide reductase / Ribonucleotide reductase small subunit


Mass: 38619.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nrdB, aq_1505 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O67475, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M citrate pH 4.0, 1.0 M lithium chloride, 20 % PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.1→65 Å / Num. obs: 26676 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.99 / Net I/σ(I): 8.9
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 1295 / CC1/2: 0.94

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ci4

5ci4


Resolution: 2.1→47.37 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.438 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2665 1309 5 %RANDOM
Rwork0.2168 ---
obs0.21948 24986 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å2-0 Å20 Å2
2--1.55 Å20 Å2
3----3.11 Å2
Refinement stepCycle: 1 / Resolution: 2.1→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2731 0 2 111 2844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132824
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172672
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.6483824
X-RAY DIFFRACTIONr_angle_other_deg1.2731.5776141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9015326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01522.989174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.2215515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1471518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023194
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02706
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.5446.211298
X-RAY DIFFRACTIONr_mcbond_other5.5456.2081297
X-RAY DIFFRACTIONr_mcangle_it7.599.2951626
X-RAY DIFFRACTIONr_mcangle_other7.5889.2971627
X-RAY DIFFRACTIONr_scbond_it5.746.661525
X-RAY DIFFRACTIONr_scbond_other5.7386.6611526
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2519.7992199
X-RAY DIFFRACTIONr_long_range_B_refined10.31972.4323435
X-RAY DIFFRACTIONr_long_range_B_other10.3172.373418
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 81 -
Rwork0.368 1817 -
obs--100 %

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