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- PDB-3n3a: Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia co... -

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Basic information

Entry
Database: PDB / ID: 3n3a
TitleRibonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI
Components
  • Protein nrdI
  • Ribonucleoside-diphosphate reductase 2 subunit beta
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / four-helix bundle / dimanganese cluster / flavoprotein
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
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, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family ...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, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Flavodoxin domain / Ribonucleotide reductase-like / Flavoprotein-like superfamily / Ferritin-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / : / Protein NrdI / Ribonucleoside-diphosphate reductase 2 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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)108,51510
Polymers107,3834
Non-polymers1,1326
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-35 kcal/mol
Surface area32160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.863, 90.678, 143.837
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonucleoside-diphosphate reductase 2 subunit beta / 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
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growpH: 7
Details: 20% PEG 3000, 0.1 M HEPES pH 7, 0.2 M lithium sulfate, 3 mM sodium dithionite

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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: Mar 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.99→29.58 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: 1.99→29.58 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.737 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3406 5.1 %RANDOM
Rwork0.203 ---
obs0.204 67011 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.36 Å2 / Biso mean: 35.252 Å2 / Biso min: 9.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.99→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6619 0 66 280 6965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226851
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.9679315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.95821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59524.03335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3881548
X-RAY DIFFRACTIONr_chiral_restr0.0790.21010
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215256
X-RAY DIFFRACTIONr_mcbond_it0.461.54107
X-RAY DIFFRACTIONr_mcangle_it0.90426623
X-RAY DIFFRACTIONr_scbond_it1.43332744
X-RAY DIFFRACTIONr_scangle_it2.3814.52691
LS refinement shellResolution: 1.99→2.045 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 242 -
Rwork0.249 4372 -
all-4614 -
obs--94.01 %
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)
10.16870.1345-0.01530.46380.1230.35530.01280.029-0.0010.0024-0.00410.02850.00260-0.00870.07010.01850.00660.0899-0.01360.10928.395230.912210.0948
20.9405-0.11920.27981.9132-0.03572.61460.08820.0728-0.02970.41240.0538-0.02670.34670.1798-0.1420.21670.0475-0.0530.0184-0.0110.072212.28428.966928.4423
30.22450.3449-0.06780.85840.3410.67030.0672-0.04080.01170.1032-0.0530.0094-0.00130.086-0.01420.0777-0.0081-0.02070.1003-0.01240.087522.528455.486529.9114
42.33040.6059-1.18331.4268-0.55684.13370.023-0.0587-0.1398-0.13040.0332-0.1116-0.31160.429-0.05620.0788-0.10230.04560.153-0.06260.055641.125764.960410.8071
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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