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- PDB-3n3b: Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia co... -

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Basic information

Entry
Database: PDB / ID: 3n3b
TitleRibonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI with a Trapped Peroxide
Components
  • Protein nrdI
  • Ribonucleoside-diphosphate reductase 2 subunit betaRibonucleotide reductase
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / four-helix bundle / dimanganese cluster / flavoprotein / peroxide
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 / protein modification process / FMN binding / manganese ion binding / DNA replication
Similarity search - Function
Ribonucleotide reductase, class Ib, NrdI, bacterial / Ribonucleotide reductase Class Ib, NrdI / NrdI Flavodoxin like / 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, class Ib, NrdI, bacterial / Ribonucleotide reductase Class Ib, NrdI / NrdI Flavodoxin like / 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 / Flavodoxin domain / Ferritin-like superfamily / Flavoprotein-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / : / HYDROGEN PEROXIDE / Protein NrdI / Ribonucleoside-diphosphate reductase 2 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
B: Ribonucleoside-diphosphate reductase 2 subunit beta
C: Protein nrdI
A: Ribonucleoside-diphosphate reductase 2 subunit beta
D: Protein nrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,58312
Polymers107,3834
Non-polymers1,2008
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-34 kcal/mol
Surface area33360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.723, 91.348, 144.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules BACD

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


Mass: 36475.070 Da / Num. of mol.: 2
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: Protein Protein nrdI


Mass: 17216.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nrdI, ygaO, b2674, JW2649 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A772

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Non-polymers , 4 types, 170 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O2
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.32 Å3/Da / Density % sol: 47 %

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.35→40.56 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N39

3n39


Resolution: 2.36→40.56 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.889 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.302 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1958 5 %RANDOM
Rwork0.234 ---
obs0.236 39152 93.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.11 Å2 / Biso mean: 33.897 Å2 / Biso min: 5.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2---0.24 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.36→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 70 162 6882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226880
X-RAY DIFFRACTIONr_angle_refined_deg0.8191.9689351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0225824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76323.929336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.952151145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2111550
X-RAY DIFFRACTIONr_chiral_restr0.0530.21013
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215278
X-RAY DIFFRACTIONr_mcbond_it0.1651.54123
X-RAY DIFFRACTIONr_mcangle_it0.30426650
X-RAY DIFFRACTIONr_scbond_it0.2432757
X-RAY DIFFRACTIONr_scangle_it0.4254.52700
LS refinement shellResolution: 2.356→2.417 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 129 -
Rwork0.287 2381 -
all-2510 -
obs--82.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.35510.15990.05690.4077-0.12660.33190.00690.02240.0276-0.0095-0.0113-0.02310.020.01820.00440.04040.01020.00330.07810.01160.0781-9.0951-31.063710.1623
21.1981-0.0609-0.56642.27360.59043.34590.1495-0.05060.05710.1941-0.03240.0268-0.2654-0.1206-0.11710.09440.01250.03920.01360.00080.0467-12.9034-9.236928.3272
30.25240.13230.05820.7831-0.16780.65890.0366-0.04380.00840.051-0.04-0.03860.0702-0.03850.00350.0543-0.01130.00510.07910.00890.0482-22.7297-55.775429.9714
42.85831.3431.58813.3579-0.30464.68190.021-0.07570.1301-0.37750.19670.22020.2996-0.3468-0.21760.0982-0.0815-0.05340.07650.04820.0441-41.6509-65.697411.0892
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B-10 - 9999
2X-RAY DIFFRACTION2C-10 - 9999
3X-RAY DIFFRACTION3A-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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