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- PDB-1pfr: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA CHAIN -

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Basic information

Entry
Database: PDB / ID: 1pfr
TitleRIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA CHAIN
ComponentsPROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE
KeywordsREDUCTASE / OXIDOREDUCTASE / DNA REPLICATION / IRON / ACTING ON RIBOSE 2'-OH
Function / homology
Function and homology information


ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / iron ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / Ribonucleoside-diphosphate reductase 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLogan, D.T. / Su, X.D. / Aberg, A. / Regnstrom, K. / Hajdu, J. / Eklund, H. / Nordlund, P.
Citation
Journal: Structure / Year: 1996
Title: Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at a dinuclear iron site.
Authors: Logan, D.T. / Su, X.D. / Aberg, A. / Regnstrom, K. / Hajdu, J. / Eklund, H. / Nordlund, P.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2
Authors: Nordlund, P. / Eklund, H.
History
DepositionDec 3, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE
B: PROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,00414
Polymers79,1762
Non-polymers1,82812
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-259 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.300, 85.500, 115.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.824533, 0.547277, 0.14364), (0.546319, 0.70398, 0.453816), (0.147243, 0.452659, -0.879442)
Vector: 20.215, -26.724, 76.528)

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Components

#1: Protein PROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE / RNR R2


Mass: 39587.883 Da / Num. of mol.: 2 / Mutation: S211A
Source method: isolated from a genetically manipulated source
Details: DIFERROUS FORM OF NON-HEME DINUCLEAR IRON SITE / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PGP1-2/PTB2 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1009
References: UniProt: P69924, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 34 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: HANGING DROP VAPOR DIFFUSION. CRYSTALLISED FROM 20% PEG 4000, 0.2M NACL, 0.1M MES PH 6.0, 1MM ETHYLMERCURY SALICYLATE., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
122 %PEG40001reservoir
20.2 M1reservoirNaCl
350 mMMES1reservoir
41 mMethylmercury thiosalicylate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 95516 / % possible obs: 86 % / Observed criterion σ(I): 0 / Redundancy: 2.79 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 1.8 / % possible all: 34.1
Reflection
*PLUS
Num. obs: 34220 / Num. measured all: 95516
Reflection shell
*PLUS
% possible obs: 34.1 %

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DIFERRIC FORM OF R2 PROTEIN, PDB ENTRY 1RIB

1rib


Resolution: 2.2→15 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: THE STRUCTURE WAS REFINED FURTHER TO THAT DESCRIBED IN REFERENCE 1 USING TNT.
RfactorNum. reflection% reflection
Rwork0.179 --
obs-34219 89 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 149.6 Å2 / ksol: 0.507 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 12 219 5807
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01157042.2
X-RAY DIFFRACTIONt_angle_deg1.95877141.2
X-RAY DIFFRACTIONt_dihedral_angle_d17.25233620
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0091685
X-RAY DIFFRACTIONt_gen_planes0.01180410
X-RAY DIFFRACTIONt_it1.25569640
X-RAY DIFFRACTIONt_nbd0.0153660
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.2520
X-RAY DIFFRACTIONt_plane_restr0.01110

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