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- PDB-7ail: Ribonucleotide Reductase R2m protein from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 7ail
TitleRibonucleotide Reductase R2m protein from Aquifex aeolicus
ComponentsRibonucleoside-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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsRehling, D. / Scaletti, E.R. / Stenmark, P.
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 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Structure summary
Category: diffrn_radiation_wavelength / diffrn_source ...diffrn_radiation_wavelength / diffrn_source / entity / entity_name_com / pdbx_seq_map_depositor_info
Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list ..._diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Apr 20, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
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
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,1702
Polymers42,1141
Non-polymers561
Water3,477193
1
A: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules

A: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3404
Polymers84,2282
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area6160 Å2
ΔGint-63 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.409, 69.409, 178.292
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 / Ribonucleotide reductase / Ribonucleotide reductase small subunit


Mass: 42113.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / 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.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.55 Å3/Da / Density % sol: 51.75 %
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: 1.73→69.4 Å / Num. obs: 46576 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.99 / Net I/σ(I): 17.4
Reflection shellResolution: 1.73→1.77 Å / Num. unique obs: 3385 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ci4

5ci4


Resolution: 1.73→54.83 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.702 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26739 2297 5 %RANDOM
Rwork0.22277 ---
obs0.22507 43386 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.824 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20 Å2
2--1.17 Å20 Å2
3----2.34 Å2
Refinement stepCycle: 1 / Resolution: 1.73→54.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 1 193 2917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132866
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172645
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.6483886
X-RAY DIFFRACTIONr_angle_other_deg1.3371.5716145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3823.029175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82215529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4911518
X-RAY DIFFRACTIONr_chiral_restr0.0790.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023207
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02643
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_it3.4053.9331319
X-RAY DIFFRACTIONr_mcbond_other3.3943.9311318
X-RAY DIFFRACTIONr_mcangle_it4.6035.8841661
X-RAY DIFFRACTIONr_mcangle_other4.6025.8861662
X-RAY DIFFRACTIONr_scbond_it4.0184.3741546
X-RAY DIFFRACTIONr_scbond_other4.0174.3751547
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0516.3922226
X-RAY DIFFRACTIONr_long_range_B_refined7.57245.7983480
X-RAY DIFFRACTIONr_long_range_B_other7.54445.5483443
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 152 -
Rwork0.458 3116 -
obs--96.69 %

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