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- PDB-9hbc: A. vinelandii nitrogenase MoFe protein Anc2 -

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Basic information

Entry
Database: PDB / ID: 9hbc
TitleA. vinelandii nitrogenase MoFe protein Anc2
Components
  • MoFe nitrogenase subunit D
  • Nitrogenase molybdenum-iron protein beta chain
KeywordsOXIDOREDUCTASE / Nitrogen fixation
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase molybdenum-iron protein beta chain, N-terminal / Domain of unknown function (DUF3364) / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / : / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase
Similarity search - Domain/homology
FE(8)-S(7) CLUSTER / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / Nitrogenase molybdenum-iron protein beta chain
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.816 Å
AuthorsDetemple, F. / Kacar, B. / Einsle, O.
Funding supportEuropean Union, Germany, United States, France, 6items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
German Research Foundation (DFG) Germany
European Research Council (ERC)310656European Union
National Aeronautics and Space Administration (NASA, United States)NNH23ZDA001N United States
National Aeronautics and Space Administration (NASA, United States)80NSSC17K0296 United States
Human Frontier Science Program (HFSP)RGY0072/2021 France
Citation
Journal: Elife / Year: 2025
Title: Structural evolution of nitrogenase over 3 billion years.
Authors: Cuevas Zuviria, B. / Detemple, F. / Amritkar, K. / Garcia, A.K. / Seefeldt, L. / Einsle, O. / Kacar, B.
#1: Journal: Elife / Year: 2025
Title: Structural evolution of nitrogenase enzymes over geologic time
Authors: Cuevas-Zuviria, B. / Detemple, F. / Amritkar, K. / Garcia, A.K. / Seefeldt, L.C. / Einsle, O. / Kacar, B.
History
DepositionNov 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MoFe nitrogenase subunit D
B: Nitrogenase molybdenum-iron protein beta chain
C: MoFe nitrogenase subunit D
D: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,80715
Polymers230,1824
Non-polymers3,62511
Water23,3831298
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32390 Å2
ΔGint-244 kcal/mol
Surface area58680 Å2
Unit cell
Length a, b, c (Å)74.936, 130.133, 209.137
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
32B
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSLYSLYSAA4 - 48113 - 490
211LYSLYSLYSLYSCC4 - 48113 - 490
322SERSERARGARGBB2 - 5232 - 523
422SERSERARGARGDD2 - 5232 - 523

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein MoFe nitrogenase subunit D


Mass: 55555.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii DJ (bacteria)
#2: Protein Nitrogenase molybdenum-iron protein beta chain / Dinitrogenase / Nitrogenase component I


Mass: 59535.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii DJ (bacteria) / References: UniProt: P07329, nitrogenase

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Non-polymers , 7 types, 1309 molecules

#3: Chemical ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CFe7MoS9 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1298 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 44.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 4.5% (w/v) of polyethylene glycol 2000, 3350, 4000 and polyethylene glycol mono methylether 5000, 0.1 M MES/NaOH at pH 6.5, 10% (v/v) of ethylene glycol and 0.15 M Mg acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.816→110.49 Å / Num. obs: 121997 / % possible obs: 95 % / Redundancy: 13 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2 / Net I/σ(I): 10
Reflection shellResolution: 1.816→2.013 Å / Rmerge(I) obs: 1.642 / Num. unique obs: 6101 / CC1/2: 0.698 / Rpim(I) all: 0.478

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.816→110.489 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.455 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.186
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 6145 5.037 %RANDOM
Rwork0.1762 115852 --
all0.179 ---
obs-121997 66.086 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.546 Å2
Baniso -1Baniso -2Baniso -3
1-0.191 Å20 Å20 Å2
2--0.073 Å20 Å2
3----0.264 Å2
Refinement stepCycle: LAST / Resolution: 1.816→110.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15926 0 112 1298 17336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01216602
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615456
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.85122565
X-RAY DIFFRACTIONr_angle_other_deg0.571.77735721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79652026
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.342598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.474102900
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg9.043103
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.49910770
X-RAY DIFFRACTIONr_chiral_restr0.0820.22354
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023788
X-RAY DIFFRACTIONr_nbd_refined0.2220.23602
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.215053
X-RAY DIFFRACTIONr_nbtor_refined0.1820.28177
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.28200
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.21209
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1290.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1020.213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.215
X-RAY DIFFRACTIONr_nbd_other0.230.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.212
X-RAY DIFFRACTIONr_mcbond_it2.2592.588066
X-RAY DIFFRACTIONr_mcbond_other2.2592.588066
X-RAY DIFFRACTIONr_mcangle_it3.3384.63710098
X-RAY DIFFRACTIONr_mcangle_other3.3384.63710099
X-RAY DIFFRACTIONr_scbond_it2.9052.8488536
X-RAY DIFFRACTIONr_scbond_other2.9052.8488537
X-RAY DIFFRACTIONr_scangle_it4.5395.11212357
X-RAY DIFFRACTIONr_scangle_other4.5395.11212358
X-RAY DIFFRACTIONr_lrange_it5.86425.56319401
X-RAY DIFFRACTIONr_lrange_other5.78225.25119115
X-RAY DIFFRACTIONr_ncsr_local_group_10.0610.0516361
X-RAY DIFFRACTIONr_ncsr_local_group_20.0490.0518006
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.061020.05009
12AX-RAY DIFFRACTIONLocal ncs0.061020.05009
23AX-RAY DIFFRACTIONLocal ncs0.049010.05009
24AX-RAY DIFFRACTIONLocal ncs0.049010.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.816-1.8630.344340.2884290.292135290.9240.9413.42230.287
1.863-1.9140.288400.29910040.298131980.9460.9357.91030.291
1.914-1.9690.299930.27120330.272128320.9310.94616.5680.261
1.969-2.030.3411920.28835020.291124770.9190.93829.60650.276
2.03-2.0970.2962730.2851060.281120600.9350.94244.6020.262
2.097-2.170.3163510.27565910.277116650.9250.94759.51140.257
2.17-2.2520.2764210.25176480.253112980.9480.95771.41970.23
2.252-2.3440.2844580.23482700.237109360.9480.96379.80980.207
2.344-2.4480.275210.21489910.217104120.9540.9791.35610.185
2.448-2.5680.2674680.20993940.21299930.9530.97198.68910.179
2.568-2.7060.2634900.19390480.19795440.9570.97699.93710.164
2.706-2.870.2374630.17685700.17990330.9670.9811000.151
2.87-3.0680.2264360.16780630.1785020.9660.98399.96470.142
3.068-3.3140.2243710.16875520.1779290.9690.98399.92430.148
3.314-3.630.2213520.15969690.16273210.970.9861000.146
3.63-4.0580.1873060.14363540.14566600.9790.9891000.134
4.058-4.6850.1642980.12256240.12459250.9850.99299.94940.118
4.685-5.7350.162860.12347370.12550230.9870.9921000.123
5.735-8.10.1911870.13437670.13639540.9830.9911000.133
8.1-110.4890.1691050.14322000.14423130.9760.97699.65410.16

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