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- PDB-9hbn: A. vinelandii nitrogenase MoFe protein Anc1b -

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Basic information

Entry
Database: PDB / ID: 9hbn
TitleA. vinelandii nitrogenase MoFe protein Anc1b
Components(MoFe nitrogenase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Nitrogen fixation
Function / homologyFE(8)-S(7) CLUSTER / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / S-1,2-PROPANEDIOL
Function and homology information
Biological speciesAzotobacter vinelandii DJ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.824 Å
AuthorsDetemple, F. / Kacar, B. / Einsle, O.
Funding supportEuropean Union, Germany, United States, France, 6items
OrganizationGrant numberCountry
European Research Council (ERC)101141673European Union
European Research Council (ERC)310656European Union
German Research Foundation (DFG) Germany
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 7, 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: MoFe nitrogenase subunit K
C: MoFe nitrogenase subunit D
D: MoFe nitrogenase subunit K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,01917
Polymers233,3734
Non-polymers3,64513
Water12,412689
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32920 Å2
ΔGint-288 kcal/mol
Surface area57740 Å2
Unit cell
Length a, b, c (Å)77.083, 128.984, 209.445
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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MoFe nitrogenase subunit ... , 2 types, 4 molecules ACBD

#1: Protein MoFe nitrogenase subunit D


Mass: 56675.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii DJ (bacteria)
#2: Protein MoFe nitrogenase subunit K


Mass: 60011.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii DJ (bacteria)

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Non-polymers , 7 types, 702 molecules

#3: Chemical ChemComp-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS9 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES/imidazole at pH 6.5, 12.5% of (w/v) of polyethylene glycol 1000, 3350 and (v/v) 2-methyl-2,4-pentandiol each and 0.02 M of 1,6-hexanediol, 1-butanol, 1,4-butanediol, (RS)-1,2- ...Details: 0.1 M MES/imidazole at pH 6.5, 12.5% of (w/v) of polyethylene glycol 1000, 3350 and (v/v) 2-methyl-2,4-pentandiol each and 0.02 M of 1,6-hexanediol, 1-butanol, 1,4-butanediol, (RS)-1,2-propanediol, 2-propanol, and 1,3-propanediol, each

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.824→109.828 Å / Num. obs: 91363 / % possible obs: 94.4 % / Redundancy: 13.1 % / CC1/2: 0.997 / Rpim(I) all: 0.068 / Net I/σ(I): 7.5
Reflection shellResolution: 1.824→2.105 Å / Rmerge(I) obs: 1.419 / Num. unique obs: 4568 / CC1/2: 0.727 / Rpim(I) all: 0.401

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.824→109.828 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.726 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.279
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 4516 4.943 %RANDOM
Rwork0.2063 86847 --
all0.209 ---
obs-91363 49.109 %-
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: 24.338 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å2-0 Å2-0 Å2
2---0.365 Å20 Å2
3---1.665 Å2
Refinement stepCycle: LAST / Resolution: 1.824→109.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15974 0 112 689 16775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01216748
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615491
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.85322773
X-RAY DIFFRACTIONr_angle_other_deg0.5831.77835863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.26152046
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.919588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.874102949
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.79910792
X-RAY DIFFRACTIONr_chiral_restr0.1150.22361
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219643
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023798
X-RAY DIFFRACTIONr_nbd_refined0.2270.23995
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.215655
X-RAY DIFFRACTIONr_nbtor_refined0.1830.28123
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.28363
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2929
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0910.29
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.215
X-RAY DIFFRACTIONr_nbd_other0.250.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.190.24
X-RAY DIFFRACTIONr_mcbond_it0.9551.3438121
X-RAY DIFFRACTIONr_mcbond_other0.9551.3438121
X-RAY DIFFRACTIONr_mcangle_it1.5982.41310188
X-RAY DIFFRACTIONr_mcangle_other1.5982.41310189
X-RAY DIFFRACTIONr_scbond_it1.3541.4778627
X-RAY DIFFRACTIONr_scbond_other1.3541.4778628
X-RAY DIFFRACTIONr_scangle_it2.2912.64912477
X-RAY DIFFRACTIONr_scangle_other2.2912.64912478
X-RAY DIFFRACTIONr_lrange_it3.9712.98119509
X-RAY DIFFRACTIONr_lrange_other3.91712.919367
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
1.824-1.8710.47580.4211910.423136370.690.8391.45930.419
1.871-1.9220.449210.365710.363133060.8610.9054.44910.355
1.922-1.9780.289440.3128720.311129380.9330.9357.07990.306
1.978-2.0390.339550.31411870.315125120.9190.9329.92650.3
2.039-2.1060.314790.29115540.292121710.9340.94313.41710.268
2.106-2.1790.3361240.27622590.279118230.9290.9520.15560.254
2.179-2.2620.3041480.26830210.27114030.9420.95327.79090.241
2.262-2.3540.2862110.26942630.27109300.9430.95540.93320.233
2.354-2.4590.3322960.25957820.263105550.930.95857.58410.226
2.459-2.5790.313830.25665570.259100950.9380.9668.74690.221
2.579-2.7180.3054090.24771500.2595850.9420.96478.86280.208
2.718-2.8830.3294030.24278950.24691030.9360.96691.15680.204
2.883-3.0820.2983840.22481370.22785750.9460.97199.37030.188
3.082-3.3280.2933480.20576320.20879870.9490.97699.91240.178
3.328-3.6460.2473750.19169810.19373740.9660.9899.75590.171
3.646-4.0750.2213350.16563830.16867210.9740.98599.95540.155
4.075-4.7050.2273310.15355930.15759290.9740.98899.91570.156
4.705-5.7590.2252680.17147990.17450680.9760.98699.98030.176
5.759-8.1340.2691920.18338110.18740030.9640.9831000.193
8.134-109.8280.2151020.17322100.17523280.9720.98199.31270.203
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)
10.105-0.0064-0.01580.00250.00930.4342-0.0191-0.07150.03690.0186-0.0054-0.00390.0535-0.09590.02440.21210.0051-0.01780.1654-0.02090.017825.728-6.02347.304
20.24490.01490.02430.0091-0.00860.3665-0.0352-0.00840.0530.02260.0053-0.0141-0.1052-0.01110.030.18340.0086-0.03390.0763-0.01440.056240.76711.4527.696
30.044-0.01180.07070.0059-0.04380.5005-0.01560.07110.0008-0.0048-0.008-0.0033-0.1046-0.06940.02360.22840.01250.0090.2055-0.00630.00525.6685.868-21.287
40.2063-0.07240.05790.06060.02590.3057-0.01090.02150.0075-0.0281-0.0057-0.02230.03280.00360.01660.1555-0.01390.02180.124-0.00210.020340.701-11.621-1.733
Refinement TLS groupSelection: ALL

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