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- PDB-1w69: Crystal Structure of Mouse Ribonucleotide Reductase Subunit R2 un... -

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Basic information

Entry
Database: PDB / ID: 1w69
TitleCrystal Structure of Mouse Ribonucleotide Reductase Subunit R2 under Reducing Conditions. A Fully Occupied Dinuclear Iron Cluster and Bound Acetate.
ComponentsRIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M2 CHAIN
KeywordsREDUCTASE / RIBONUCLEOTIDE REDUCTASE / DNA REPLICATION / DIIRON OXYGEN PROTEIN / TYROSYL RADICAL / METAL-BINDING / OXIDOREDUCTASE
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 / nuclear envelope / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / : / Ribonucleoside-diphosphate reductase subunit M2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKarlsen, S. / Strand, K.R. / Kolberg, M. / Rohr, A.K. / Gorbitz, C.H. / Andersson, K.K.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structural Studies of Changes in the Native Dinuclear Iron Center of Ribonucleotide Reductase Protein R2 from Mouse
Authors: Strand, K.R. / Karlsen, S. / Kolberg, M. / Rohr, A.K. / Gorbitz, C.H. / Andersson, K.K.
History
DepositionAug 16, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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
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_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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3214
Polymers45,1501
Non-polymers1723
Water97354
1
A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M2 CHAIN
hetero molecules

A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6438
Polymers90,2992
Non-polymers3436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
MethodPQS
Unit cell
Length a, b, c (Å)75.993, 107.454, 91.929
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 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M2 CHAIN / RIBONUCLEOTIDE REDUCTASE R2 / RIBONUCLEOTIDE REDUCTASE SMALL CHAIN


Mass: 45149.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET-3A-M2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: P11157, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: PROVIDES THE PRECURSORS NECESSARY FOR DNA SYNTHESIS. CATALYTIC ACTIVITY: 2'- ...FUNCTION: PROVIDES THE PRECURSORS NECESSARY FOR DNA SYNTHESIS. CATALYTIC ACTIVITY: 2'-DEOXYRIBONUCLEOSIDE DIPHOSPHATE + OXIDIZED THIOREDOXIN + H(2)O = RIBONUCLEOSIDE DIPHOSPHATE + REDUCED 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: 2.88 Å3/Da / Density % sol: 56.9 %
Crystal growpH: 6 / Details: 0.1 M SODIUM ACETATE PH 4.7, 1.2 M SODIUM CHLORIDE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.01681
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01681 Å / Relative weight: 1
ReflectionResolution: 2.2→23.9 Å / Num. obs: 18053 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 5.5 / % possible all: 97.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XSM

1xsm


Resolution: 2.2→21.8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1326398.86 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 891 4.9 %RANDOM
Rwork0.217 ---
obs0.217 18040 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.2529 Å2 / ksol: 0.392597 e/Å3
Displacement parametersBiso mean: 55.3 Å2
Baniso -1Baniso -2Baniso -3
1-9.25 Å20 Å20 Å2
2--0.94 Å20 Å2
3----10.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→21.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 6 54 2383
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it2.42
X-RAY DIFFRACTIONc_scangle_it3.62.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 144 5.3 %
Rwork0.293 2573 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5ACY.PARAMACY.TOP

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