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- PDB-1rlr: STRUCTURE OF RIBONUCLEOTIDE REDUCTASE PROTEIN R1 -

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Basic information

Entry
Database: PDB / ID: 1rlr
TitleSTRUCTURE OF RIBONUCLEOTIDE REDUCTASE PROTEIN R1
ComponentsRIBONUCLEOTIDE REDUCTASE PROTEIN R1
KeywordsOXIDOREDUCTASE / REDUCTASE (ACTING ON CH2)
Function / homology
Function and homology information


ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / DNA replication / ATP binding ...ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / DNA replication / ATP binding / identical protein binding / cytosol
Similarity search - Function
Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / 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, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / 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 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase 1 subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsUhlin, U. / Eklund, H.
Citation
Journal: Nature / Year: 1994
Title: Structure of ribonucleotide reductase protein R1.
Authors: Uhlin, U. / Eklund, H.
#1: Journal: FEBS Lett. / Year: 1993
Title: Crystallization and Crystallographic Investigations of Ribonucleotide Reductase Protein R1 from Escherichia Coli
Authors: Uhlin, U. / Uhlin, T. / Eklund, H.
History
DepositionAug 12, 1994Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEOTIDE REDUCTASE PROTEIN R1


Theoretical massNumber of molelcules
Total (without water)86,0101
Polymers86,0101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)226.000, 226.000, 341.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein RIBONUCLEOTIDE REDUCTASE PROTEIN R1 / RIBONUCLEOSIDE DIPHOSPHATE REDUCTASE PROTEIN R1 (B1 IN OLD TEXTS)


Mass: 86010.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: 293 / Gene (production host): NRDA / Production host: Escherichia coli (E. coli)
References: UniProt: P00452, ribonucleoside-diphosphate reductase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity % sol: 63 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop / Details: Uhlin, U., (1993) FEBS Lett., 336, 148.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 %lithium sulphate1reservoir
210 mMmagnesium sulphate1reservoir
325 mMsodium citrate1reservoir
415 mg/mlprotein1drop
58.5 %lithium sulphate1drop
65 mMmagnesium sulphate1drop
712.5 mMsodium citrate1drop

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Data collection

RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 109500 / % possible obs: 94 %
Reflection
*PLUS
Highest resolution: 2.5 Å / Rmerge(I) obs: 0.098

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→7 Å / σ(F): 1.1 /
RfactorNum. reflection
Rwork0.21 -
obs0.21 104230
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5875 0 0 234 6109
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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