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- PDB-6gp2: Ribonucleotide Reductase class Ie R2 from Mesoplasma florum, DOPA... -

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Basic information

Entry
Database: PDB / ID: 6gp2
TitleRibonucleotide Reductase class Ie R2 from Mesoplasma florum, DOPA-active form
ComponentsRibonucleoside-diphosphate reductase beta chain
KeywordsOXIDOREDUCTASE / ribonucleotide reduction / subunit beta / ferritin-like superfamily / DOPA modification
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / membrane / metal ion binding
Similarity search - Function
Ribonucleoside-diphosphate reductase subunit beta / 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
Similarity search - Component
Biological speciesMesoplasma florum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsSrinivas, V. / Lebrette, H. / Lundin, D. / Kutin, Y. / Sahlin, M. / Lerche, M. / Enrich, J. / Branca, R.M.M. / Cox, N. / Sjoberg, B.M. / Hogbom, M.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research Council2017-04018 Sweden
European Research CouncilHIGH-GEAR 724394 Sweden
Knut and Alice Wallenberg Foundation2012.0233 Sweden
Knut and Alice Wallenberg Foundation2017.0275 Sweden
CitationJournal: Nature / Year: 2018
Title: Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens.
Authors: Srinivas, V. / Lebrette, H. / Lundin, D. / Kutin, Y. / Sahlin, M. / Lerche, M. / Eirich, J. / Branca, R.M.M. / Cox, N. / Sjoberg, B.M. / Hogbom, M.
History
DepositionJun 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Jan 17, 2024Group: 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
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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase beta chain
B: Ribonucleoside-diphosphate reductase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7694
Polymers79,6892
Non-polymers802
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-58 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.162, 53.744, 79.284
Angle α, β, γ (deg.)90.00, 108.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribonucleoside-diphosphate reductase beta chain


Mass: 39844.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesoplasma florum (strain ATCC 33453 / NBRC 100688 / NCTC 11704 / L1) (bacteria)
Strain: ATCC 33453 / NBRC 100688 / NCTC 11704 / L1 / Gene: Mfl530 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6F0T5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100-200 mM calcium acetate, 100 mM ammonium sulfate, 15-20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
ReflectionResolution: 1.479→42.73 Å / Num. obs: 117391 / % possible obs: 99.82 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06584 / Rpim(I) all: 0.02774 / Rrim(I) all: 0.07158 / Net I/σ(I): 12.67
Reflection shellResolution: 1.479→1.532 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.403 / Mean I/σ(I) obs: 1.17 / Num. unique obs: 11678 / CC1/2: 0.613 / Rpim(I) all: 0.6017 / Rrim(I) all: 1.53 / % possible all: 99.65

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: 000)refinement
XDSVERSION Jan 26, 2018data reduction
XDSVERSION Jan 26, 2018data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DHZ

3dhz


Resolution: 1.48→42.73 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.61
RfactorNum. reflection% reflectionSelection details
Rfree0.185 5862 5 %random selection
Rwork0.154 ---
obs-117311 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39 Å2
Refinement stepCycle: LAST / Resolution: 1.48→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5177 0 2 522 5701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065787
X-RAY DIFFRACTIONf_angle_d0.87919
X-RAY DIFFRACTIONf_dihedral_angle_d23.5962161
X-RAY DIFFRACTIONf_chiral_restr0.071846
X-RAY DIFFRACTIONf_plane_restr0.0051039
LS refinement shellResolution: 1.4792→1.532 Å
RfactorNum. reflection% reflection
Rfree0.4083 582 -
Rwork0.3738 11659 -
obs--100 %
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)
13.7476-2.44160.70151.583-0.25990.422-0.08660.0879-0.14120.34090.0297-0.12320.31830.0543-0.14530.6024-0.0960.00880.27550.04940.3362-26.59819.472234.8205
20.52030.03760.02091.018-0.20022.13260.0394-0.00550.00730.0299-0.0484-0.01920.016-0.08030.01210.21810.01040.01710.1228-0.0070.178-22.958931.153211.023
31.95421.90560.23915.9440.80463.4094-0.01330.07380.1224-0.3599-0.00330.0837-0.3186-0.37920.00340.32420.06030.00230.23910.02650.2049-32.097238.044-8.8607
45.30252.9208-3.71233.18211.04428.68450.01070.0988-0.1449-0.2257-0.0280.18250.2555-0.1869-0.15520.2315-0.0259-0.00510.1768-0.03490.2229-30.449619.1985-2.1715
50.6296-0.03620.10822.6942-0.542.13430.02020.0438-0.03670.038-0.0413-0.07640.2590.01360.02540.22440.01150.02490.13-0.01280.1845-16.89424.9615.6378
60.5995-1.51871.68816.1947-6.42497.47760.13660.0161-0.1488-0.260.06820.25790.4931-0.0304-0.19750.38370.0120.02210.137-0.01140.2245-20.356110.7088-1.5765
71.4304-0.133-0.31162.27720.95712.64420.01110.0998-0.0722-0.4925-0.3298-0.60940.3510.46480.42640.27830.0210.05990.19910.03240.2773-13.021623.2608-6.2251
81.1723-0.5342-0.10415.1991-0.63130.99540.0466-0.04790.16950.2464-0.1524-1.05930.06260.50760.05820.27120.033-0.00780.38780.0830.4198-7.243227.63031.005
95.4689-0.90631.50513.44450.66011.9635-0.04380.32160.3282-0.441-0.2120.531-0.1196-0.6440.00160.22920.0652-0.030.4149-0.02370.2403-42.487333.5606-3.9441
100.91850.1590.36960.3454-0.02813.4130.0561-0.14080.03740.1381-0.0180.0622-0.0525-0.332-0.03580.27560.00390.0420.1863-0.00830.1781-29.862132.881225.0376
113.37733.88831.41244.50111.54021.78110.2256-0.6693-0.39740.3168-0.2605-0.1360.5793-0.2644-0.00540.5138-0.08340.00760.37730.09350.2412-26.851318.849743.1071
124.2249-0.61752.87342.6893-0.62531.97120.1132-0.2842-0.42650.15330.05730.1760.6748-0.8823-0.19350.4092-0.19890.07190.5230.01630.2633-42.915520.093431.5666
132.41840.35250.85720.64980.00453.09350.0835-0.10310.05960.1839-0.00650.1348-0.1212-0.6195-0.05690.33530.01910.08580.345-0.02630.2215-38.398836.147730.0357
143.6102-0.4422.08271.6392-1.57914.41980.1827-0.2222-0.25630.11860.10260.45840.1639-1.121-0.25430.3298-0.06280.09620.78160.00450.343-52.367828.725132.0931
155.1188-1.10983.54641.2663-2.71768.8273-0.0979-0.36140.22310.3985-0.14950.1537-0.328-0.89410.21660.48140.04530.08230.5802-0.09180.2668-44.70635.983840.7358
162.55620.73190.35721.77470.86940.52540.198-0.76830.56440.6507-0.16650.0159-0.1608-0.7321-0.09670.71330.17750.11340.9082-0.10050.3907-44.649642.649543.3421
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -5 THROUGH 20 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 21 THROUGH 133 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 134 THROUGH 149 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 150 THROUGH 164 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 165 THROUGH 230 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 231 THROUGH 261 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 262 THROUGH 286 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 287 THROUGH 340 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID -2 THROUGH 20 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 21 THROUGH 133 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 134 THROUGH 149 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 150 THROUGH 164 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 165 THROUGH 230 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 231 THROUGH 262 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 263 THROUGH 286 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 287 THROUGH 340 )

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