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- PDB-1h0n: Cobalt substitution of mouse R2 ribonucleotide reductase to model... -

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Basic information

Entry
Database: PDB / ID: 1h0n
TitleCobalt substitution of mouse R2 ribonucleotide reductase to model the reactive diferrous state
ComponentsRIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE
KeywordsOXIDOREDUCTASE / RIBONUCLEOTIDE REDUCTASE / DINUCLEAR METAL-CLUSTER
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: 2.4 Å
AuthorsStrand, K.R. / Karlsen, S. / Andersson, K.K.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Cobalt Substitution of Mouse R2 Ribonucleotide Reductase as a Model for Thereactive Diferrous State. Spectroscopic and Structural Evidence for a Ferromagnetically Coupled Dinuclear Cobalt Cluster
Authors: Strand, K.R. / Karlsen, S. / Andersson, K.K.
History
DepositionJun 26, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2673
Polymers45,1501
Non-polymers1182
Water2,018112
1
A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE
hetero molecules

A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5356
Polymers90,2992
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)75.100, 106.860, 91.460
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 / RIBONUCLEOTIDE REDUCTASE SMALL CHAIN


Mass: 45149.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COBALT-SUBSTITUTED / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P11157, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDNA SYNTHESIS PRECURSOR PROVIDER

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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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growpH: 6
Details: 0.1 M NA-ACETATE BUFFER PH4.7, 1.2 M NACL, 7.5 MG/ML APO-R2 PROTEIN. CRYSTALS WERE SOAKED IN 5 MM CO2+ SOLUTION, PH INCREASED TO 6
Crystal grow
*PLUS
pH: 4.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.5 mg/mlprotein1drop
20.1 Msodium acetate1reservoirpH4.7
31.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9312
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9312 Å / Relative weight: 1
ReflectionResolution: 2.37→30 Å / Num. obs: 18915 / % possible obs: 99.9 % / Redundancy: 2.4 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.6
Reflection shellResolution: 2.37→2.48 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.71 / % possible all: 99
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 15274 / % possible obs: 99.3 % / Rmerge(I) obs: 0.095

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XSM

1xsm


Resolution: 2.4→8 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.297 691 5 %RANDOM
Rwork0.218 ---
obs0.218 14006 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.7287 Å2 / ksol: 0.34365 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.44 Å20 Å20 Å2
2--1.85 Å20 Å2
3----6.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 2 112 2494
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.024
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_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.42
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 116 5 %
Rwork0.277 2190 -
obs--95.1 %
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.42

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