PDB-9hb9: A. vinelandii nitrogenase MoFe protein Anc1a

ID or keywords:

Entry

Database: PDB / ID: 9hb9

Title

A. vinelandii nitrogenase MoFe protein Anc1a

Components

MoFe nitrogenase subunit D
Nitrogenase molybdenum-iron protein beta chain

Keywords

OXIDOREDUCTASE / 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

Biological species

Azotobacter vinelandii DJ (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.658 Å

Authors

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

Funding support

European Union,

Germany,

United States,

France, 6items

Organization	Grant number	Country
European Research Council (ERC)	310656	European Union
German Research Foundation (DFG)		Germany
European Research Council (ERC)		European Union
National Aeronautics and Space Administration (NASA, United States)	80NSSC17K0296	United States
National Aeronautics and Space Administration (NASA, United States)	NNH23ZDA001N	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.

History

Deposition	Nov 5, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 10, 2025	Provider: repository / Type: Initial release
Revision 1.1	Oct 1, 2025	Group: Database references / Category: citation / citation_author

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9hb9.cif.gz	422.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9hb9.ent.gz	326.7 KB	Display	PDB format
PDBx/mmJSON format	9hb9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9hb9_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	9hb9_full_validation.pdf.gz	2.7 MB	Display
Data in XML	9hb9_validation.xml.gz	76.1 KB	Display
Data in CIF	9hb9_validation.cif.gz	100.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hb/9hb9 ftp://data.pdbj.org/pub/pdb/validation_reports/hb/9hb9	HTTPS FTP

-
Related structure data

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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#26 - Feb 2002 Nitrogenase similarity (12)

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

236 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)	70.290, 138.615, 208.581
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
3	2	B
4	2	D

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LYS	LYS	A	A	5 - 481	15 - 491
2	1	1	LYS	LYS	C	C	5 - 481	15 - 491
3	2	2	ARG	ARG	B	B	2 - 523	2 - 523
4	2	2	ARG	ARG	D	D	2 - 523	2 - 523

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4

-
Protein , 2 types, 4 molecules ACBD

#1: Protein	MoFe nitrogenase subunit D Mass: 56933.480 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

-
Non-polymers , 5 types, 142 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-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.61 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M LiSO4 x 1 H2O, 0.1 M bis-Tris/HCl at pH 6.5, 25%(w/v) of polyethylene glycol 3350

-
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: Feb 17, 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: 2.638→19.879 Å / Num. obs: 46401 / % possible obs: 93.7 % / Redundancy: 12.8 % / CC_1/2: 0.989 / R_merge(I) obs: 0.368 / R_pim(I) all: 0.106 / Net I/σ(I): 7.1
Reflection shell	Resolution: 2.658→2.912 Å / Num. unique obs: 2321 / CC_1/2: 0.425 / % possible all: 51.8

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
autoPROC		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.658→19.879 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.907 / SU B: 16.171 / SU ML: 0.301 / Cross valid method: FREE R-VALUE / ESU R Free: 0.393
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2202	2377	5.123 %
R_work	0.169	44024	-
all	0.172	-	-
obs	-	46401	77.828 %

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: 41.992 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.251 Å²	0 Å²	-0 Å²
2-	-	-0.279 Å²	-0 Å²
3-	-	-	0.028 Å²

Refinement step

Cycle: LAST / Resolution: 2.658→19.879 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15942	0	96	134	16172

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.012	16491
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	15271
X-RAY DIFFRACTION	r_angle_refined_deg	1.267	1.851	22363
X-RAY DIFFRACTION	r_angle_other_deg	0.454	1.778	35298
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.368	5	1994
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.4	5	88
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.777	10	2880
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	9.007	10	14
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.877	10	771
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	2328
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	19184
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3734
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	3621
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	15336
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	8115
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	8302
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	427
X-RAY DIFFRACTION	r_metal_ion_refined	0.123	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.204	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.205	0.2	68
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.153	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.161	4.106	7988
X-RAY DIFFRACTION	r_mcbond_other	2.161	4.105	7988
X-RAY DIFFRACTION	r_mcangle_it	3.523	7.378	9978
X-RAY DIFFRACTION	r_mcangle_other	3.523	7.378	9979
X-RAY DIFFRACTION	r_scbond_it	2.579	4.404	8502
X-RAY DIFFRACTION	r_scbond_other	2.579	4.404	8503
X-RAY DIFFRACTION	r_scangle_it	4.328	7.999	12277
X-RAY DIFFRACTION	r_scangle_other	4.327	7.999	12278
X-RAY DIFFRACTION	r_lrange_it	6.265	38.503	18491
X-RAY DIFFRACTION	r_lrange_other	6.264	38.508	18487
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.076	0.05	16219
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.067	0.05	17811

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07619	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07619	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06684	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06684	0.0501

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
2.658-2.726	0.343	11	0.358	188	0.357	4290	0.922	0.867	4.6387	0.352
2.726-2.799	0.372	18	0.356	322	0.357	4174	0.894	0.898	8.1457	0.355
2.799-2.878	0.33	49	0.303	944	0.305	4039	0.927	0.939	24.5853	0.302
2.878-2.965	0.297	107	0.283	2315	0.284	3923	0.939	0.943	61.7385	0.282
2.965-3.06	0.31	178	0.268	3154	0.27	3869	0.933	0.948	86.1204	0.262
3.06-3.165	0.287	181	0.246	3475	0.248	3681	0.938	0.956	99.3208	0.235
3.165-3.281	0.288	194	0.219	3392	0.223	3586	0.942	0.967	100	0.205
3.281-3.411	0.242	177	0.201	3297	0.203	3474	0.961	0.974	100	0.186
3.411-3.558	0.225	156	0.174	3181	0.176	3337	0.966	0.98	100	0.157
3.558-3.726	0.217	162	0.157	3054	0.16	3216	0.968	0.983	100	0.141
3.726-3.919	0.182	141	0.144	2886	0.146	3027	0.977	0.986	100	0.126
3.919-4.147	0.216	161	0.127	2746	0.132	2907	0.971	0.989	100	0.113
4.147-4.42	0.178	136	0.123	2599	0.126	2735	0.979	0.99	100	0.111
4.42-4.754	0.184	125	0.127	2435	0.13	2560	0.979	0.99	100	0.115
4.754-5.179	0.202	118	0.132	2256	0.136	2374	0.974	0.99	100	0.121
5.179-5.741	0.22	129	0.15	2058	0.155	2187	0.976	0.988	100	0.136
5.741-6.539	0.216	105	0.15	1860	0.154	1965	0.974	0.987	100	0.135
6.539-7.801	0.172	91	0.135	1621	0.137	1712	0.983	0.989	100	0.128
7.801-10.269	0.164	79	0.132	1315	0.134	1395	0.987	0.991	99.9283	0.134
10.269-19.879	0.21	59	0.193	926	0.194	985	0.972	0.985	100	0.2

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 2 types, 4 molecules ACBD

-
Non-polymers , 5 types, 142 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 2 types, 4 molecules ACBD

-Non-polymers , 5 types, 142 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 2 types, 4 molecules ACBD

-
Non-polymers , 5 types, 142 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi