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

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Basic information

Entry
Database: PDB / ID: 6cwp
TitleX-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) ribonucleotide reductase beta subunit (anaerobic)
Components
  • Ribonucleotide reductase
  • VAL-GLU-TYR-THR-LYS-HIS
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / four-helix bundle / dimanganese cluster / oxidoretuctase
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: 1.92 Å
AuthorsMaggiolo, A.O. / Rose, H.R. / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
F: VAL-GLU-TYR-THR-LYS-HIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5197
Polymers72,2993
Non-polymers2204
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-42 kcal/mol
Surface area25180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.455, 53.455, 220.747
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Ribonucleotide reductase


Mass: 35760.559 Da / Num. of mol.: 2 / Fragment: \cf3 \cf0
Source method: isolated from a genetically manipulated source
Details: tag removed for crystallization
Source: (gene. exp.) Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / UW101) (bacteria)
Strain: ATCC 17061 / DSM 2064 / UW101 / Gene: Fjoh_4066 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5FCJ5
#2: Protein/peptide VAL-GLU-TYR-THR-LYS-HIS


Mass: 777.864 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Flavobacterium johnsoniae (bacteria)
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.52 Å3/Da / Density % sol: 51.16 % / Mosaicity: 0.369 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M magnesium acetate, 20% (w/v) PEG 3350

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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: Jun 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 53468 / % possible obs: 99 % / Redundancy: 5 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.04 / Rrim(I) all: 0.095 / Χ2: 1.041 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.92-1.953.70.81423360.5470.4290.9270.79288.1
1.95-1.993.90.7326110.6480.3820.830.79794.3
1.99-2.034.30.60226400.7220.3140.6840.82197.9
2.03-2.074.50.4926870.8240.2510.5540.856100
2.07-2.114.70.44427370.8210.2270.5010.869100
2.11-2.164.80.37726480.860.1910.4250.847100
2.16-2.224.80.30527500.9090.1540.3430.85100
2.22-2.284.90.25926510.9380.1290.290.879100
2.28-2.344.80.23527120.9410.1180.2640.87100
2.34-2.424.90.20126950.9590.10.2250.873100
2.42-2.514.90.17626870.9680.0860.1970.89100
2.51-2.6150.15426930.9740.0740.1720.909100
2.61-2.725.10.13227250.9830.0640.1480.963100
2.72-2.875.10.10826530.9860.0510.120.998100
2.87-3.055.10.09627120.9890.0450.1061.087100
3.05-3.285.20.09127100.9870.0430.1011.381100
3.28-3.615.40.07827030.9910.0360.0861.562100
3.61-4.145.70.06627190.9940.030.0721.596100
4.14-5.216.40.05426850.9960.0230.0591.30399.9
5.21-506.60.04727140.9980.0190.0511.10299.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.89 / SU B: 4.135 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.171
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 2367 5.1 %RANDOM
Rwork0.2057 ---
obs0.2077 44358 86.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87 Å2 / Biso mean: 24.173 Å2 / Biso min: 6.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 1.92→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5059 0 4 68 5131
Biso mean--11.11 17.29 -
Num. residues----613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195178
X-RAY DIFFRACTIONr_bond_other_d0.0010.024893
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9437006
X-RAY DIFFRACTIONr_angle_other_deg0.818311260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4865610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01324.644267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38315916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2911523
X-RAY DIFFRACTIONr_chiral_restr0.0760.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021235
LS refinement shellResolution: 1.919→1.969 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 76 -
Rwork0.258 1362 -
all-1438 -
obs--35.7 %

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