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- PDB-3n37: Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 3n37
TitleRibonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli
ComponentsRibonucleoside-diphosphate reductase 2 subunit betaRibonucleotide reductase
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / four-helix bundle / dimanganese cluster
Function / homology
Function and homology information


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 / manganese ion binding
Similarity search - Function
Ribonucleoside-diphosphate reductase subunit beta / 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 ...Ribonucleoside-diphosphate reductase subunit beta / 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
: / Ribonucleoside-diphosphate reductase 2 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBoal, A.K. / Cotruvo Jr., J.A. / Stubbe, J. / Rosenzweig, A.C.
CitationJournal: Science / Year: 2010
Title: Structural basis for activation of class Ib ribonucleotide reductase.
Authors: Boal, A.K. / Cotruvo, J.A. / Stubbe, J. / Rosenzweig, A.C.
History
DepositionMay 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6774
Polymers36,4751
Non-polymers2023
Water7,206400
1
A: Ribonucleoside-diphosphate reductase 2 subunit beta
hetero molecules

A: Ribonucleoside-diphosphate reductase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3548
Polymers72,9502
Non-polymers4046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area3590 Å2
ΔGint-17 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.142, 78.142, 266.754
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-557-

HOH

21A-586-

HOH

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Components

#1: Protein Ribonucleoside-diphosphate reductase 2 subunit beta / Ribonucleotide reductase / Ribonucleotide reductase 2 / R2F protein


Mass: 36475.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2676, JW2651, nrdF, ygaD / Production host: Escherichia coli (E. coli)
References: UniProt: P37146, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growpH: 7.5 / Details: 0.1 M HEPES pH 7.5, 30% PEG 4000

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→67.67 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R2F

1r2f


Resolution: 1.65→67.67 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 2.571 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2902 5.1 %RANDOM
Rwork0.167 ---
obs0.168 57359 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.99 Å2 / Biso mean: 19.543 Å2 / Biso min: 4.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20.46 Å20 Å2
2--0.92 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.65→67.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 8 400 2703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222473
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.9643390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3185321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.83325.207121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05515434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7631510
X-RAY DIFFRACTIONr_chiral_restr0.0750.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211907
X-RAY DIFFRACTIONr_mcbond_it0.4711.51484
X-RAY DIFFRACTIONr_mcangle_it0.95322421
X-RAY DIFFRACTIONr_scbond_it1.7693989
X-RAY DIFFRACTIONr_scangle_it3.0134.5951
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 198 -
Rwork0.328 3850 -
all-4048 -
obs--94.69 %
Refinement TLS params.Method: refined / Origin x: 20.4162 Å / Origin y: 26.4494 Å / Origin z: -10.7832 Å
111213212223313233
T0.0696 Å2-0.0109 Å20.0296 Å2-0.0145 Å2-0.015 Å2--0.0452 Å2
L0.8255 °2-0.0503 °20.2031 °2-0.3519 °20.22 °2--0.6823 °2
S0.0905 Å °-0.0428 Å °0.083 Å °0.0267 Å °-0.0492 Å °-0.013 Å °-0.0356 Å °-0.0388 Å °-0.0413 Å °

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