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- PDB-6cwq: X-ray crystal structure of Flavobacterium johnsoniae dimanganese(... -

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Basic information

Entry
Database: PDB / ID: 6cwq
TitleX-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) ribonucleotide reductase beta subunit (as-isolated)
ComponentsRibonucleotide reductase
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / four-helix bundle / dimanganese cluster
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / membrane / metal ion binding / cytosol
Similarity search - Function
Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRose, H.R. / Maggiolo, A.O. / Boal, A.K.
CitationJournal: Biochemistry / Year: 2018
Title: Structural Basis for Superoxide Activation of Flavobacterium johnsoniae Class I Ribonucleotide Reductase and for Radical Initiation by Its Dimanganese Cofactor.
Authors: Rose, H.R. / Ghosh, M.K. / Maggiolo, A.O. / Pollock, C.J. / Blaesi, E.J. / Hajj, V. / Wei, Y. / Rajakovich, L.J. / Chang, W.C. / Han, Y. / Hajj, M. / Krebs, C. / Silakov, A. / Pandelia, M.E. ...Authors: Rose, H.R. / Ghosh, M.K. / Maggiolo, A.O. / Pollock, C.J. / Blaesi, E.J. / Hajj, V. / Wei, Y. / Rajakovich, L.J. / Chang, W.C. / Han, Y. / Hajj, M. / Krebs, C. / Silakov, A. / Pandelia, M.E. / Bollinger, J.M. / Boal, A.K.
History
DepositionMar 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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: Ribonucleotide reductase
B: Ribonucleotide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9988
Polymers71,7292
Non-polymers2686
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-53 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.356, 50.816, 79.285
Angle α, β, γ (deg.)106.150, 105.030, 95.750
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ribonucleotide reductase


Mass: 35864.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / UW101) (bacteria)
Strain: ATCC 17061 / DSM 2064 / UW101 / Gene: Fjoh_4066 / Plasmid: pPR-IBA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5FCJ5
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 20% PEG 3350, 100 mM magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→72.63 Å / Num. obs: 51916 / % possible obs: 96 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.035 / Rrim(I) all: 0.066 / Χ2: 0.76 / Net I/σ(I): 8.8 / Num. measured all: 175305
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.933.30.526320.8050.3130.5920.62994.9
1.93-1.973.30.37725150.8840.2370.4460.63295
1.97-2.013.40.33225850.8880.2070.3920.65295
2.01-2.053.30.26525410.9310.1670.3140.66994.9
2.05-2.093.40.22726170.930.1430.2690.795.7
2.09-2.143.40.19826000.9570.1230.2330.67495.8
2.14-2.193.40.16725880.9690.1040.1970.795.6
2.19-2.253.40.13825490.9770.0850.1620.6995.9
2.25-2.323.40.12226150.9840.0760.1440.68896
2.32-2.393.40.1126210.9860.0690.130.70496.2
2.39-2.483.40.09125460.9910.0570.1080.68895.8
2.48-2.583.40.07925910.9920.0490.0930.69795.9
2.58-2.73.40.06926410.9940.0430.0810.71496.2
2.7-2.843.40.05826090.9960.0360.0680.74696.6
2.84-3.023.40.05226140.9960.0320.0610.77796.7
3.02-3.253.40.04425990.9970.0270.0520.86996.6
3.25-3.583.40.03725940.9980.0230.0430.95196.5
3.58-4.093.40.03126160.9980.0190.0371.03996.6
4.09-5.163.40.02826250.9980.0170.0331.02996.9
5.16-503.40.02326180.9990.0140.0270.93196.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→72.63 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.421 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 2636 5.1 %RANDOM
Rwork0.192 ---
obs0.193 49280 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.17 Å2 / Biso mean: 23.417 Å2 / Biso min: 11.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å2-0.4 Å2-0.75 Å2
2--0.98 Å20.05 Å2
3----0.96 Å2
Refinement stepCycle: final / Resolution: 1.9→72.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 0 6 163 5191
Biso mean--23.23 25.98 -
Num. residues----610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195197
X-RAY DIFFRACTIONr_bond_other_d0.0010.024897
X-RAY DIFFRACTIONr_angle_refined_deg0.981.9437053
X-RAY DIFFRACTIONr_angle_other_deg0.758311294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8945634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09524.757267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92315920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2611522
X-RAY DIFFRACTIONr_chiral_restr0.0610.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025873
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021241
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 210 -
Rwork0.266 3507 -
all-3717 -
obs--91.53 %

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