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- PDB-6y1x: X-ray structure of the radical SAM protein NifB, a key nitrogenas... -

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Basic information

Entry
Database: PDB / ID: 6y1x
TitleX-ray structure of the radical SAM protein NifB, a key nitrogenase maturating enzyme
ComponentsRadical SAM domain protein
KeywordsMETAL BINDING PROTEIN / Carbide synthase FeMo-co NifB-co FeS cluster Assembly machinery metalloprotein
Function / homology
Function and homology information


catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Nitrogenase cofactor biosynthesis protein NifB / MoaA/NifB/PqqE, iron-sulphur binding, conserved site / moaA / nifB / pqqE family signature. / : / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Nitrogenase cofactor biosynthesis protein NifB / MoaA/NifB/PqqE, iron-sulphur binding, conserved site / moaA / nifB / pqqE family signature. / : / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Radical SAM domain protein
Similarity search - Component
Biological speciesMethanothrix thermoacetophila (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.95 Å
AuthorsSosa-Fajardo, A. / Legrand, P. / Paya-Tormo, L. / Martin, L. / Pellicer-Martinez, M.T. / Echavarri-Erasun, C. / Vernede, X. / Rubio, L.M. / Nicolet, Y.
Funding support France, Spain, 4items
OrganizationGrant numberCountry
French National Research AgencyANR-17-EURE-0003 France
French National Research AgencyANR-10-INBS-05-02 France
French National Research AgencyANR-15-IDEX-02 France
Spanish Ministry of Science, Innovation, and Universities2017-88475-R Spain
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Structural Insights into the Mechanism of the Radical SAM Carbide Synthase NifB, a Key Nitrogenase Cofactor Maturating Enzyme.
Authors: Fajardo, A.S. / Legrand, P. / Paya-Tormo, L.A. / Martin, L. / Pellicer Marti Nez, M.T. / Echavarri-Erasun, C. / Vernede, X. / Rubio, L.M. / Nicolet, Y.
History
DepositionFeb 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Radical SAM domain protein
B: Radical SAM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,54813
Polymers70,5902
Non-polymers1,95811
Water7,152397
1
A: Radical SAM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2266
Polymers35,2951
Non-polymers9315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Radical SAM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3227
Polymers35,2951
Non-polymers1,0276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.180, 48.680, 80.380
Angle α, β, γ (deg.)78.810, 87.730, 89.940
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Radical SAM domain protein


Mass: 35294.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothrix thermoacetophila (strain DSM 6194 / JCM 14653 / NBRC 101360 / PT) (archaea)
Gene: Mthe_0422 / Production host: Escherichia coli (E. coli) / References: UniProt: A0B690
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, Bis-Tris-HCl, ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.7389 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7389 Å / Relative weight: 1
ReflectionResolution: 1.9→47.76 Å / Num. obs: 38738 / % possible obs: 81.9 % / Redundancy: 3.3 % / CC1/2: 0.993 / Net I/σ(I): 7
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 952 / CC1/2: 0.37

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
SHELXDEphasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.95→47.754 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 23.04
RfactorNum. reflection% reflection
Rfree0.2121 1889 4.9 %
Rwork0.1769 --
obs0.1786 38552 88.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.76 Å2 / Biso mean: 32.667 Å2 / Biso min: 10.43 Å2
Refinement stepCycle: final / Resolution: 1.95→47.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3982 0 59 397 4438
Biso mean--45.28 38.81 -
Num. residues----504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-2.00270.335750.3005147346
2.0027-2.06170.3334950.2697215368
2.0617-2.12820.29851330.2329286488
2.1282-2.20430.24031480.2176287391
2.2043-2.29250.2481560.207292192
2.2925-2.39690.23151570.189295392
2.3969-2.52320.23871460.1795298493
2.5232-2.68130.2251610.1677301695
2.6813-2.88830.2091530.1698303095
2.8883-3.17890.18511680.1736304497
3.1789-3.63880.1881650.1576309497
3.6388-4.58390.18331650.1478311398
4.5839-47.7540.19791670.1697314599
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)
13.69353.92154.02455.36653.07087.68810.00181.2957-0.6879-0.03590.17240.17681.0054-0.0338-0.21870.5822-0.0407-0.00540.6347-0.09650.450135.59397.428158.8017
22.39450.02-1.37042.4487-1.3644.7766-0.03240.0505-0.07340.02220.0119-0.08670.05760.30320.01450.1372-0.0004-0.03930.17020.02190.156748.256813.537576.432
37.95411.85211.63565.69691.2221.9552-0.08891.2311-0.1811-1.16380.0737-1.01780.02880.9281-0.05590.3983-0.00590.05540.5750.0490.250253.373617.023856.7173
42.50680.16170.99814.2601-1.48383.47750.02050.7261-0.3865-0.5852-0.0138-0.22190.3942-0.0086-0.09970.1981-0.0368-0.00420.3662-0.05230.207944.778314.154863.2563
52.82870.1114-1.38351.9256-0.23335.24130.01090.59260.3177-0.2935-0.04770.0002-0.36790.0875-0.01680.197-0.0019-0.02480.26850.0750.211540.598923.757264.0063
62.31720.970.9521.14260.68321.9686-0.0047-0.02250.10470.0956-0.05350.05120.0097-0.03150.05190.07690.0326-0.01950.0828-0.0070.157535.013617.979781.6803
71.62431.1286-0.01691.04861.0044.2913-0.06260.02840.1886-0.06430.14050.1608-0.6132-0.07990.05710.14360.0192-0.02610.13560.0260.230331.730923.680181.8302
83.2698-0.70821.50510.9517-0.10682.20060.04580.0642-0.21520.09930.03180.12960.05360.0709-0.08820.1456-0.0203-0.00440.10470.00580.152731.74998.001179.2293
94.6172-0.70333.30093.0677-3.18316.17460.09940.3466-0.696-0.35740.1408-0.10280.65610.3308-0.15440.2835-0.0159-0.01590.2149-0.08290.313527.677-1.753174.9006
102.7905-0.69591.83987.6085-0.68332.47340.1695-1.5862-0.71940.62540.2454-0.33710.80470.4611-0.2540.5020.0867-0.01770.77590.12480.481558.197616.79239.7245
112.47780.73470.78650.72611.42573.04860.137-0.7013-0.3234-0.0771-0.175-0.14730.65280.09380.01080.21780.0503-0.0020.2870.04530.198945.049922.470431.2245
124.92730.9468-1.75553.8104-0.14085.00330.0899-0.0915-0.16020.0418-0.06890.2278-0.00920.0249-0.02750.145-0.0066-0.04730.1815-0.03190.20544.638919.725418.0918
131.69760.42480.51830.50041.24525.20790.1268-0.36460.06150.1983-0.28010.23270.1328-0.62780.15260.26150.01720.0170.3812-0.030.23736.529724.026136.2643
143.3304-0.14520.63622.1303-0.45766.12090.1198-0.3133-0.33560.1099-0.04260.28330.58980.0945-0.16570.15650.01370.00040.1926-0.0180.195845.82422.729734.3287
152.3313-0.3697-1.04432.9815-0.7518.19580.028-0.81150.58120.27240.1288-0.0686-0.71870.1527-0.14490.24320.0091-0.02410.3969-0.12760.280244.439333.819536.7034
161.81050.15210.35520.8918-0.51453.17330.0226-0.28050.16250.0915-0.0672-0.0663-0.2392-0.10810.02070.13550.0054-0.02110.1414-0.01210.176654.216729.080324.1212
171.8454-1.0554-0.31591.2963-1.40934.2615-0.133-0.10050.29510.02010.0196-0.0504-0.42010.16140.14110.1545-0.01970.00110.106-0.03630.190358.733132.405816.0924
183.03530.57231.3790.7384-0.04242.4976-0.0020.0366-0.2059-0.02940.078-0.07710.02170.0451-0.09220.13080.0233-0.01210.09960.00180.186158.901116.615118.4503
195.99021.89753.26577.65423.81967.94550.2734-0.3899-0.63970.4069-0.01310.09440.7589-0.364-0.32180.2606-0.0076-0.03580.21260.07080.286263.27067.610423.2331
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 42 )A20 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 76 )A43 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 90 )A77 - 90
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 108 )A91 - 108
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 146 )A109 - 146
6X-RAY DIFFRACTION6chain 'A' and (resid 147 through 174 )A147 - 174
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 199 )A175 - 199
8X-RAY DIFFRACTION8chain 'A' and (resid 200 through 252 )A200 - 252
9X-RAY DIFFRACTION9chain 'A' and (resid 253 through 271 )A253 - 271
10X-RAY DIFFRACTION10chain 'B' and (resid 20 through 35 )B20 - 35
11X-RAY DIFFRACTION11chain 'B' and (resid 36 through 50 )B36 - 50
12X-RAY DIFFRACTION12chain 'B' and (resid 51 through 68 )B51 - 68
13X-RAY DIFFRACTION13chain 'B' and (resid 69 through 90 )B69 - 90
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 108 )B91 - 108
15X-RAY DIFFRACTION15chain 'B' and (resid 109 through 121 )B109 - 121
16X-RAY DIFFRACTION16chain 'B' and (resid 122 through 174 )B122 - 174
17X-RAY DIFFRACTION17chain 'B' and (resid 175 through 199 )B175 - 199
18X-RAY DIFFRACTION18chain 'B' and (resid 200 through 252 )B200 - 252
19X-RAY DIFFRACTION19chain 'B' and (resid 253 through 271 )B253 - 271

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