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- PDB-2bq1: Ribonucleotide reductase class 1b holocomplex R1E,R2F from Salmon... -

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Basic information

Entry
Database: PDB / ID: 2bq1
TitleRibonucleotide reductase class 1b holocomplex R1E,R2F from Salmonella typhimurium
Components
  • RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 ALPHA SUBUNIT
  • RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 BETA SUBUNIT
KeywordsOXIDOREDUCTASE / R1 / R2 / R1E / R2F / IRON / CLASS 1B / HOLOCOMPLEX / ALLOSTERIC REGULATION / RIBONUCLEOTIDE REDUCTASE / ATP-BINDING / METAL-BINDING / DNA REPLICATION / RADICAL TRANSFER / ALLOSTERIC ENZYME / ASYMMETRIC COMPLEX / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / ATP binding / metal ion binding
Similarity search - Function
50s Ribosomal Protein L19e, Chain O, domain 1 - #20 / Ribonucleotide reductase N-terminal / Ribonucleotide reductase, class 1b, subunit NrdE / Ribonucleotide reductase N-terminal / Ribonucleoside-diphosphate reductase subunit beta / 50s Ribosomal Protein L19e, Chain O, domain 1 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal ...50s Ribosomal Protein L19e, Chain O, domain 1 - #20 / Ribonucleotide reductase N-terminal / Ribonucleotide reductase, class 1b, subunit NrdE / Ribonucleotide reductase N-terminal / Ribonucleoside-diphosphate reductase subunit beta / 50s Ribosomal Protein L19e, Chain O, domain 1 / 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 / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / : / Ribonucleoside-diphosphate reductase 2 subunit beta / Ribonucleoside-diphosphate reductase 2 subunit alpha
Similarity search - Component
Biological speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.99 Å
AuthorsUppsten, M. / Farnegardh, M. / Domkin, V. / Uhlin, U.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The First Holocomplex Structure of Ribonucleotide Reductase Gives New Insight Into its Mechanism of Action
Authors: Uppsten, M. / Farnegardh, M. / Domkin, V. / Uhlin, U.
History
DepositionApr 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2006Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Derived calculations / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 ALPHA SUBUNIT
F: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 ALPHA SUBUNIT
I: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 BETA SUBUNIT
J: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,18512
Polymers233,8984
Non-polymers1,2868
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-68.7 kcal/mol
Surface area72130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)270.372, 270.372, 270.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 ALPHA SUBUNIT / RIBONUCLEOTIDE REDUCTASE 2 / R1E PROTEIN


Mass: 80686.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q08698, ribonucleoside-diphosphate reductase
#2: Protein RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 BETA SUBUNIT / RIBONUCLEOTIDE REDUCTASE 2 / R2F PROTEIN


Mass: 36262.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P17424, ribonucleoside-diphosphate reductase
#3: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
Compound detailsCATALYTIC ACTIVITY: 2'-DEOXYRIBONUCLEOSIDE DIPHOSPHATE + THIOREDOXIN DISULFIDE + H(2)O = ...CATALYTIC ACTIVITY: 2'-DEOXYRIBONUCLEOSIDE DIPHOSPHATE + THIOREDOXIN DISULFIDE + H(2)O = RIBONUCLEOSIDE DIPHOSPHATE + THIOREDOXIN.

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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: 3.79 Å3/Da / Density % sol: 66 %
Crystal growpH: 7.5
Details: 1:1 MIX OF PROTEIN SOLUTION (8 MG/ML R1E, 4 MG/ML R2F, 1.5 MM DGTP, 1.5 MM ADP, 1.5 MM MGCL2 AND 1.5 MM HYDROXYUREA) AND RESERVOIR SOLUTION CONSISTING OF 100 MM NAHEPES PH 7.5 AND 1.8 M SODIUM FORMATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 23, 2004
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 4→40 Å / Num. obs: 29196 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 15.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.5
Reflection shellResolution: 4→4.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PEM

1pem


Resolution: 3.99→182.57 Å / Cor.coef. Fo:Fc: 0.811 / Cor.coef. Fo:Fc free: 0.778 / SU B: 53.692 / SU ML: 0.757 / Cross valid method: THROUGHOUT / ESU R Free: 0.946 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1484 5.1 %RANDOM
Rwork0.262 ---
obs0.265 27672 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 65.31 Å2
Refinement stepCycle: LAST / Resolution: 3.99→182.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15452 0 68 0 15520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02115883
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0361.94621560
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54651926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.22362
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212168
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.28393
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2597
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3931.59631
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.724215486
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.57436252
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.074.56074
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.99→4.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.345 102
Rwork0.262 2006

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