PDB-9haz: A. vinelandii nitrogenase Fe protein Anc1b

ID or keywords:

Entry

Database: PDB / ID: 9haz

Title

A. vinelandii nitrogenase Fe protein Anc1b

Components

(Fe protein NifH) x 2

Keywords

OXIDOREDUCTASE / Nitrogen fixation

Function / homology

IRON/SULFUR CLUSTER

Function and homology information

Biological species

Azotobacter vinelandii DJ (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.434 Å

Authors

Detemple, F. / Kacar, B. / Einsle, O.

Funding support

Germany, European Union,

United States,

France, 6items

Organization	Grant number	Country
German Research Foundation (DFG)		Germany
European Research Council (ERC)	310656	European Union
European Research Council (ERC)		European Union
National Aeronautics and Space Administration (NASA, United States)	80NSSC17K0296	United States
Human Frontier Science Program (HFSP)	RGY0072/2021	France
National Aeronautics and Space Administration (NASA, United States)	NNH23ZDA001N	United States

Citation

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

Deposition	Nov 5, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 10, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9haz.cif.gz	231.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9haz.ent.gz	180.3 KB	Display	PDB format
PDBx/mmJSON format	9haz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9haz_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9haz_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9haz_validation.xml.gz	46.6 KB	Display
Data in CIF	9haz_validation.cif.gz	60.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ha/9haz ftp://data.pdbj.org/pub/pdb/validation_reports/ha/9haz	HTTPS FTP

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Related structure data

Related structure data	9hb9C 9hbcC 9hbnC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Fe protein NifH

B: Fe protein NifH

C: Fe protein NifH

D: Fe protein NifH

hetero molecules

127 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	123.352, 109.784, 95.213
Angle α, β, γ (deg.)	90.000, 118.610, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-301- MG

#1: Protein	Fe protein NifH Mass: 31553.209 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii DJ (bacteria)
#2: Protein	Fe protein NifH Mass: 31567.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii DJ (bacteria)
#3: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.23 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: containing 0.1 M MES/NaOH at pH 6.5, 7.5% of (w/v) polyethylene glycol 6000, 8000, 10000 each, 10%(vol/vol) isopropanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
Detector	Type: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: May 22, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8856 Å / Relative weight: 1
Reflection	Resolution: 2.434→69.844 Å / Num. obs: 26823 / % possible obs: 74.6 % / Redundancy: 1.7 % / CC_1/2: 0.98 / R_merge(I) obs: 0.096 / R_pim(I) all: 0.09 / Net I/σ(I): 2.7
Reflection shell	Resolution: 2.434→2.611 Å / R_merge(I) obs: 0.321 / Num. unique obs: 1341 / CC_1/2: 0.716 / R_pim(I) all: 0.447

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
STARANISO		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.434→69.844 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.833 / SU B: 14.289 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / ESU R Free: 0.46
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2722	1313	4.895 %
R_work	0.195	25510	-
all	0.199	-	-
obs	-	26823	64.184 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 28.883 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.174 Å²	0 Å²	-0.133 Å²
2-	-	0.45 Å²	0 Å²
3-	-	-	-0.3 Å²

Refinement step

Cycle: LAST / Resolution: 2.434→69.844 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8699	0	19	72	8790

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	8890
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8613
X-RAY DIFFRACTION	r_angle_refined_deg	1.234	1.827	11998
X-RAY DIFFRACTION	r_angle_other_deg	0.434	1.759	19887
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.382	5	1166
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.925	5	48
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.683	10	1639
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.545	10	382
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	1374
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	10440
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1808
X-RAY DIFFRACTION	r_nbd_refined	0.197	0.2	1996
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	8953
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	4382
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	4809
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	259
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.019	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.19	0.2	7
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.251	0.2	49
X-RAY DIFFRACTION	r_nbd_other	0.225	0.2	90
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.206	0.2	9
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.075	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.597	2.86	4649
X-RAY DIFFRACTION	r_mcbond_other	1.597	2.86	4649
X-RAY DIFFRACTION	r_mcangle_it	2.735	5.138	5816
X-RAY DIFFRACTION	r_mcangle_other	2.735	5.138	5817
X-RAY DIFFRACTION	r_scbond_it	1.702	3.036	4241
X-RAY DIFFRACTION	r_scbond_other	1.701	3.036	4242
X-RAY DIFFRACTION	r_scangle_it	2.934	5.531	6158
X-RAY DIFFRACTION	r_scangle_other	2.934	5.531	6159
X-RAY DIFFRACTION	r_lrange_it	5.279	28.455	9824
X-RAY DIFFRACTION	r_lrange_other	5.279	28.462	9821

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.434-2.497	0.324	10	0.229	304	0.232	3061	0.951	0.973	10.2581	0.228
2.497-2.565	0.297	23	0.252	531	0.254	2999	0.937	0.965	18.4728	0.266
2.565-2.64	0.291	46	0.275	771	0.276	2918	0.945	0.957	27.9986	0.287
2.64-2.721	0.405	50	0.26	1106	0.266	2828	0.909	0.959	40.8769	0.269
2.721-2.81	0.304	81	0.239	1563	0.242	2761	0.94	0.964	59.5436	0.25
2.81-2.908	0.294	101	0.224	1851	0.228	2626	0.943	0.968	74.3336	0.237
2.908-3.018	0.337	104	0.21	1939	0.217	2562	0.93	0.97	79.7424	0.224
3.018-3.141	0.282	99	0.214	1951	0.217	2496	0.945	0.969	82.1314	0.228
3.141-3.28	0.341	91	0.221	1868	0.226	2364	0.924	0.967	82.868	0.241
3.28-3.44	0.299	94	0.207	1834	0.212	2282	0.94	0.972	84.4873	0.231
3.44-3.626	0.243	100	0.204	1687	0.206	2145	0.96	0.975	83.31	0.225
3.626-3.845	0.293	96	0.188	1635	0.194	2023	0.947	0.979	85.566	0.214
3.845-4.109	0.218	76	0.17	1574	0.173	1933	0.972	0.981	85.3595	0.195
4.109-4.437	0.265	79	0.16	1450	0.165	1791	0.956	0.983	85.3713	0.187
4.437-4.859	0.227	61	0.158	1347	0.161	1672	0.961	0.984	84.2105	0.189
4.859-5.429	0.271	49	0.178	1150	0.182	1479	0.953	0.981	81.0683	0.208
5.429-6.263	0.278	56	0.188	1048	0.192	1332	0.948	0.979	82.8829	0.221
6.263-7.655	0.248	44	0.177	874	0.18	1127	0.962	0.98	81.4552	0.206
7.655-10.761	0.181	32	0.162	653	0.163	875	0.974	0.981	78.2857	0.182
10.761-69.844	0.222	21	0.22	374	0.22	515	0.969	0.969	76.699	0.281

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