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- PDB-6gp3: Ribonucleotide Reductase class Ie R2 from Mesoplasma florum, inac... -

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Basic information

Entry
Database: PDB / ID: 6gp3
TitleRibonucleotide Reductase class Ie R2 from Mesoplasma florum, inactive form
ComponentsRibonucleoside-diphosphate reductase beta chain
KeywordsOXIDOREDUCTASE / ribonucleotide reduction / subunit beta / ferritin-like superfamily
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: 1.23 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
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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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)79,7374
Polymers79,6572
Non-polymers802
Water12,863714
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-60 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.193, 53.425, 79.133
Angle α, β, γ (deg.)90.00, 108.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribonucleoside-diphosphate reductase beta chain


Mass: 39828.609 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.: 714 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
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: 1.229→42.71 Å / Num. obs: 200401 / % possible obs: 98.89 % / Redundancy: 6.4 % / Biso Wilson estimate: 16.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05372 / Rpim(I) all: 0.02285 / Rrim(I) all: 0.05848 / Net I/σ(I): 15.13
Reflection shellResolution: 1.229→1.273 Å / Redundancy: 6 % / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 19641 / CC1/2: 0.661 / Rpim(I) all: 0.484 / Rrim(I) all: 1.197 / % possible all: 97.28

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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: 1.23→42.71 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.81
RfactorNum. reflection% reflectionSelection details
Rfree0.163 10018 5 %random selection
Rwork0.147 ---
obs-200307 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.28 Å2
Refinement stepCycle: LAST / Resolution: 1.23→42.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5175 0 2 714 5891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056337
X-RAY DIFFRACTIONf_angle_d0.7768692
X-RAY DIFFRACTIONf_dihedral_angle_d22.2962384
X-RAY DIFFRACTIONf_chiral_restr0.069927
X-RAY DIFFRACTIONf_plane_restr0.0061146
LS refinement shellResolution: 1.229→1.273 Å
RfactorNum. reflection% reflection
Rfree0.3434 982 -
Rwork0.3296 19622 -
obs--97 %
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)
12.87170.53141.33440.23650.1620.6871-0.1378-0.6430.41850.2843-0.0491-0.0699-0.7478-0.5358-0.00040.63560.25730.03790.7885-0.14830.3662-43.513643.370142.7084
21.7944-2.09410.61452.1018-0.67180.419-0.1502-0.212-0.11540.12490.0892-0.09440.38410.0553-0.08780.3434-0.02310.00520.270.08240.24-25.35648.887236.7667
30.3744-0.44070.30081.1412-0.20861.9680.0347-0.1511-0.16150.0416-0.0297-0.00880.2415-0.02890.03390.161-0.0125-0.01280.12620.0120.1219-22.227520.748627.1955
40.37230.02560.01110.6804-0.16841.15070.02020.04020.0383-0.07580.00570.0158-0.06-0.0936-0.02840.12930.02080.01210.12150.00270.1287-24.754335.53732.7562
51.45250.5648-0.68075.9849-5.11294.28220.01110.0355-0.1528-0.16520.11330.17320.2298-0.3174-0.27290.1904-0.0282-0.00770.1738-0.0130.1612-30.665818.4979-1.3849
60.53820.3924-0.20352.3877-0.68691.49690.00450.0288-0.0018-0.0168-0.0109-0.06350.11040.02820.01470.09540.0180.01280.0952-0.00630.1149-16.331725.03965.318
70.39780.1324-0.03485.1996-2.74842.6492-0.02670.0414-0.0552-0.2045-0.0026-0.13060.1175-0.0140.0010.14790.01440.03220.1008-0.02140.1277-17.110716.0003-3.5737
81.57290.2361-0.58492.8903-0.63980.53650.0149-0.060.01480.05350.0276-0.51220.0530.1541-0.07170.15560.0113-0.00810.19270.01990.2032-7.246127.93431.5361
92.3693-0.74490.18954.1776-0.32761.7449-0.02880.21140.1133-0.29430.05010.3249-0.0443-0.4504-0.13190.12420.0099-0.02850.26550.00470.1492-41.895532.1503-2.5393
101.157-0.00210.17790.6381-0.0592.5951-0.00460.01890.0415-0.0157-0.01080.1365-0.1399-0.38420.01570.11010.03130.01630.17680.02590.1397-36.182636.07266.9434
110.8350.16610.04020.1414-0.0282.13610.0834-0.4270.10050.1441-0.135-0.0077-0.1034-0.0189-0.030.213-0.05170.02060.2954-0.03350.1272-19.382836.839940.3172
121.00490.11840.30470.4356-0.20722.32180.0711-0.1663-0.04050.07810.0040.02980.0333-0.1871-0.06480.1302-0.00640.01830.1628-0.00230.117-30.48129.140128.8935
136.84183.90081.68683.31921.56910.79160.1743-0.585-0.34490.1783-0.1605-0.1050.3042-0.2234-0.04150.2604-0.0445-0.00580.33530.07550.1621-25.792819.030843.2319
143.2338-1.53092.96862.217-1.60585.94140.3511-0.2484-0.3524-0.0880.08920.23510.5651-0.6689-0.42370.2193-0.11640.01190.37840.05250.2424-43.325320.363129.5183
151.135-0.0714-0.27620.8891-0.31660.90.0468-0.20430.11680.13960.01590.1089-0.1157-0.3457-0.06020.17630.02170.04780.261-0.01830.1339-37.814936.381731.4635
162.4876-1.00133.11781.4118-2.15825.18290.1089-0.1691-0.15860.00570.16240.29160.063-0.7083-0.23350.17960.00280.04930.55380.04530.2356-50.516128.520333.8996
174.5846-1.37863.52030.7775-0.99662.7327-0.1199-0.29720.09330.1734-0.02110.1438-0.3062-0.37620.18570.25570.04120.03240.3043-0.04990.1457-43.083335.752642.3999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 287 THROUGH 340 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID -5 THROUGH 20 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 21 THROUGH 49 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 50 THROUGH 148 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 149 THROUGH 167 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 168 THROUGH 230 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 231 THROUGH 286 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 287 THROUGH 340 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID -1 THROUGH 20 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 21 THROUGH 49 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 50 THROUGH 70 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 71 THROUGH 133 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 134 THROUGH 148 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 149 THROUGH 167 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 168 THROUGH 230 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 231 THROUGH 261 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 262 THROUGH 286 )

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