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- PDB-1xsm: PROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE FROM MOUSE -

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Basic information

Entry
Database: PDB / ID: 1xsm
TitlePROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE FROM MOUSE
ComponentsRIBONUCLEOTIDE REDUCTASE R2
KeywordsOXIDOREDUCTASE / DNA REPLICATION / IRON
Function / homology
Function and homology information


deoxyribonucleotide metabolic process / Interconversion of nucleotide di- and triphosphates / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein heterotetramerization / blastocyst development ...deoxyribonucleotide metabolic process / Interconversion of nucleotide di- and triphosphates / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein heterotetramerization / blastocyst development / positive regulation of G1/S transition of mitotic cell cycle / ferric iron binding / protein homodimerization activity / nucleoplasm / identical protein binding / cytosol
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 subunit M2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKauppi, B. / Nielsen, B.N. / Ramaswamy, S. / Kjoller-Larsen, I. / Thelander, M. / Thelander, L. / Eklund, H.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: The three-dimensional structure of mammalian ribonucleotide reductase protein R2 reveals a more-accessible iron-radical site than Escherichia coli R2.
Authors: Kauppi, B. / Nielsen, B.B. / Ramaswamy, S. / Larsen, I.K. / Thelander, M. / Thelander, L. / Eklund, H.
#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
DepositionJul 3, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...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.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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
Revision 1.4May 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: RIBONUCLEOTIDE REDUCTASE R2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2052
Polymers45,1501
Non-polymers561
Water1,62190
1
A: RIBONUCLEOTIDE REDUCTASE R2
hetero molecules

A: RIBONUCLEOTIDE REDUCTASE R2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4114
Polymers90,2992
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)77.078, 108.932, 92.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein RIBONUCLEOTIDE REDUCTASE R2 / R2


Mass: 45149.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: T7-RNA POLYMERASE / Gene: NRDD / Plasmid: PET / Gene (production host): NRDD / Production host: Escherichia coli (E. coli)
References: UniProt: P11157, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 9

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 40 %
Crystal growpH: 4.7
Details: 1.0-1.2 M NACL, 0.1 M SODIUM ACETATE, PH 4.7, 0-4% PEG4000.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Nielsen, B.B., (1995) FEBS Letters, 373, 310.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5 mg/mlprotein1drop
20.8-1.0 M1dropNaCl
350 mMacetate1drop
40.8-1.0 M1reservoirNaCl
550 mMacetate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 15, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 17131 / % possible obs: 95.87 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 17.6
Reflection shellResolution: 2.29→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.283 / % possible all: 70.9
Reflection
*PLUS
% possible obs: 95.8 % / Num. measured all: 144719
Reflection shell
*PLUS
% possible obs: 70.9 % / Rmerge(I) obs: 0.3

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RIB

1rib


Resolution: 2.3→25 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.25 1370 10 %
Rwork0.191 --
obs0.191 -95.87 %
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 90 1 2469
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg2.3
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35 Å2
Refine LS restraints
*PLUS
Type: x_dihedral_angle_deg / Dev ideal: 28.6

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