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- PDB-7jmb: Crystal structure of Nitrogenase iron-molybdenum cofactor biosynt... -

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Basic information

Entry
Database: PDB / ID: 7jmb
TitleCrystal structure of Nitrogenase iron-molybdenum cofactor biosynthesis enzyme NifB from Methanothermobacter thermautotrophicus with three Fe4S4 clusters
ComponentsNitrogenase iron-molybdenum cofactor biosynthesis protein NifB
KeywordsMETAL BINDING PROTEIN / Nitrogenase / Radical SAM enzyme / iron-molybdenum cofactor biosynthesis
Function / homology
Function and homology information


iron-sulfur cluster binding / catalytic activity / metal ion binding
Similarity search - Function
Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / FeMo cofactor biosynthesis protein NifB
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKang, W. / Rettberg, L. / Ribbe, M.W. / Hu, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM67626 United States
Department of Energy (DOE, United States)DE-SC0016510 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: X-Ray Crystallographic Analysis of NifB with a Full Complement of Clusters: Structural Insights into the Radical SAM-Dependent Carbide Insertion During Nitrogenase Cofactor Assembly.
Authors: Kang, W. / Rettberg, L.A. / Stiebritz, M.T. / Jasniewski, A.J. / Tanifuji, K. / Lee, C.C. / Ribbe, M.W. / Hu, Y.
History
DepositionJul 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 20, 2021Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Feb 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifB
B: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5748
Polymers65,4642
Non-polymers2,1106
Water0
1
A: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7874
Polymers32,7321
Non-polymers1,0553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7874
Polymers32,7321
Non-polymers1,0553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.870, 77.640, 90.800
Angle α, β, γ (deg.)90.000, 128.850, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 16 - 276 / Label seq-ID: 18 - 278

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain 'A' and (resid 16 through 36 or (resid 37...AA
2(chain 'B' and (resid 16 through 24 or (resid 25...BB

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Components

#1: Protein Nitrogenase iron-molybdenum cofactor biosynthesis protein NifB


Mass: 32731.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: O27899
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4M sodium malonate (pH7)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.71915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2019
RadiationMonochromator: Water-cooled flat double Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.71915 Å / Relative weight: 1
ReflectionResolution: 3→70.71 Å / Num. obs: 12056 / % possible obs: 90.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 78.88 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.085 / Net I/σ(I): 8.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.9 % / Num. unique obs: 1215 / CC1/2: 0.581 / Rpim(I) all: 0.704 / % possible all: 63.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y1X

6y1x


Resolution: 3→70.7 Å / SU ML: 0.5268 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.3073
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3143 1207 10.03 %
Rwork0.2622 10823 -
obs0.2675 12030 90.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70 Å2
Refinement stepCycle: LAST / Resolution: 3→70.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 48 0 3510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243601
X-RAY DIFFRACTIONf_angle_d0.61995000
X-RAY DIFFRACTIONf_chiral_restr0.0485598
X-RAY DIFFRACTIONf_plane_restr0.0053655
X-RAY DIFFRACTIONf_dihedral_angle_d7.14052102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.120.414890.3598804X-RAY DIFFRACTION61.42
3.12-3.260.43161130.3611021X-RAY DIFFRACTION77.51
3.26-3.430.39881400.31271282X-RAY DIFFRACTION96.6
3.43-3.650.33551470.30691286X-RAY DIFFRACTION96.96
3.65-3.930.33171380.27131250X-RAY DIFFRACTION94.23
3.93-4.330.30781430.2551304X-RAY DIFFRACTION97.7
4.33-4.950.28251460.23311259X-RAY DIFFRACTION94.87
4.95-6.240.33471440.25891307X-RAY DIFFRACTION96.6
6.24-70.70.25821470.22721310X-RAY DIFFRACTION95.17
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)
10.376443488303-1.09381428931-0.1300353738013.696588405871.0584642541.63924962826-0.207415774836-0.0876921416732-0.5036511464550.2257392706880.2298897492350.7533567561930.08146138535970.186289086821-0.2199789331450.3505991492430.005916880532950.220555416140.6604858073270.1542188003470.579761861191-12.629949346238.567098713820.6419156576
22.972152675621.1270840866-1.384923805593.50790020478-0.9926816213892.6824979657-0.2469191900520.4177517639010.422972985347-0.401514723740.7639924103640.645700848681-0.0294228784021-0.257797921122-0.4043981779150.418046276673-0.1085742412490.1182234937840.5001770180980.2348127416480.486846468716-17.871042607545.72615189416.9233120799
31.08144640108-0.6270169203240.02272004275931.993483783970.9611581258130.579117053424-0.009312767614690.5705070392340.0157507579657-0.408240484347-0.113569505888-0.10253739317-0.1088241287060.33595537675-0.4232142819110.423354369458-0.1529978621680.4085738847890.766151550335-0.07171115045720.461204079962-12.131706255132.100412629611.0446532175
42.10211286168-0.706611238012-1.003864893690.2703997728380.5338312223081.6755974262-0.05744682136680.662138654008-0.3800969086380.0752687264347-0.1479422426590.2090626691750.48762255892-0.3744997271881.381983479590.427027380733-0.2961261337580.5641951016450.773839440077-0.3022744331860.714760506138-8.4246803118523.61638810128.55818979837
54.354797902560.957063775753-2.195340459530.651417269938-1.193858798862.27429663294-0.5968575340690.319672053663-0.848349889309-1.15109436818-0.0974277700823-0.6780409154060.793424715810.1712787446370.9429809262750.666945120792-0.08914377338290.3253679274530.5108781026390.1256613230760.415117718739-2.9937294522924.478134547419.9440277062
61.30424242750.1870676025210.8221644791820.5009416348680.4125971465030.688103457274-0.138146167393-0.102000187834-0.5547194870760.003221710155960.464381930448-0.0591924252562-0.1094922143640.374932598545-0.009738296918310.485692835719-0.1532326648780.2583558628220.8222333506760.2036415812820.51673040048-6.5497434619232.593581901328.2436808649
72.84579630921-2.0843627544-1.631039142348.73513714397.802558992171.99936874246-0.2790528098430.7062230650590.1451272673-0.084769242853-0.453251771640.345460109985-0.08226082234550.409790851681-0.1722776413320.2858182705790.2205272600750.1168053813290.4560642848050.194504506640.252936677181-3.0132094388217.17008242747.5888728525
80.6478143537460.4870776593280.1436337043731.48262828923-0.009693376649880.163066924346-0.03003138619970.2863253797650.363395109182-0.2268952557460.00223588538353-0.0755502315823-0.114713353346-0.0448495858441-0.1904163851330.576638534069-0.384181329395-0.02763308514930.7782157788880.3354432094080.790263121127-20.60924671626.226813136552.0222145328
93.45638333975-1.767882365361.099279292272.73008211219-0.05181502544652.58451710694-0.6153843693540.383253565801-0.370332532090.784028872436-0.2639743085360.3212153778760.0791894430857-0.1329261757540.5830248642630.265013604015-0.03672895660390.1318973057970.294889389328-0.01309444935380.255177001046-20.842826942113.797303095248.949652835
100.3841836063260.489452841820.2959466296470.6604543551090.1799491793241.401624009260.134810775021-0.487198323563-0.0551006112490.680749380134-0.06455279675690.0471340901136-0.0629202650419-0.260015311909-0.00272479329370.6713205782720.2483658717240.2379540715890.7372312618760.3087800995270.267593659289-19.118128532418.422289946760.3831481761
111.25743581646-0.7955359700020.8499239268273.37729890338-0.5277964395470.569268234125-0.340017427147-0.37244092468-0.6563641910921.05254964644-0.5767494424450.07882419121140.2924161485750.9148781930630.5366326875670.6840974362290.2346293082420.163317929460.6978756719650.123143993080.412969039371-12.702872439820.692525026962.9955756978
120.8371589289710.312311622436-0.8751177501114.1216690467-3.162125513613.285156918630.591437695329-0.2654104994740.4966673778890.654991397160.4810456845780.64632385062-0.691186157573-0.226750895291-0.6538271319130.408771816961-0.04042208496930.1053673332761.07586328521-0.1778911053460.74130428336-18.634262303541.420022646258.2103731195
135.133595367411.234816417650.0562525518635.35261877392-3.385371130952.00664059653-0.0880457443731-1.035208435851.190829772370.6876579364240.5486891494850.941036391416-0.240306746597-0.846164873566-0.06870784662740.409607256328-0.01733896299250.09538077976740.613733372376-0.4016676669370.646269867841-11.439042237536.262600568564.0995965063
146.79418584397-1.154482389282.464211529823.98967865815-2.148797303193.768559747910.159223987248-0.574727825420.8437859951810.567473402356-0.557882757454-0.252067681337-0.7043701366820.4030021759260.5339618771440.335431577140.06271611879610.03769190674660.4928365113280.02704314630340.436408289761-7.6596634888735.560515469250.4605284977
154.95532129644-1.925804865836.581986573661.8535984714-1.72937482679.36876610531.047627793550.7276600495890.396928900964-0.262626222858-0.5921821192780.1563005854830.9985413280031.60871062014-0.7144215373480.5078518476790.1044602950360.1039974566290.8828108903970.1695739122190.589370925844-1.9222255461535.477846850840.7588859321
160.806374915959-0.311883884416-0.8903801245210.7025940350910.07738003820361.99958259907-0.2649409756710.237266689171-0.3543232437010.2455767515280.1305717170250.0906498531618-0.02268913091930.360721139929-0.5716924782740.5566310274240.2770526640220.3033151302360.6186448145250.07747363188520.229668048044-9.724851771321.149815572445.7426949394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 166 )
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 187 )
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 216 )
6X-RAY DIFFRACTION6chain 'A' and (resid 217 through 277 )
7X-RAY DIFFRACTION7chain 'B' and (resid 16 through 27 )
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 46 )
9X-RAY DIFFRACTION9chain 'B' and (resid 47 through 82 )
10X-RAY DIFFRACTION10chain 'B' and (resid 83 through 106 )
11X-RAY DIFFRACTION11chain 'B' and (resid 107 through 141 )
12X-RAY DIFFRACTION12chain 'B' and (resid 142 through 166 )
13X-RAY DIFFRACTION13chain 'B' and (resid 167 through 187 )
14X-RAY DIFFRACTION14chain 'B' and (resid 188 through 235 )
15X-RAY DIFFRACTION15chain 'B' and (resid 236 through 251 )
16X-RAY DIFFRACTION16chain 'B' and (resid 252 through 277 )

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