7JRF: Nitrogenase molybdenum-iron protein alpha chain

Co-co-bound nitrogenase mofe-protein from a. Vinelandii. Determined by X-ray diffraction at 1.33 Å resolution. Released 24 Mar 2021.

Method: X-ray diffraction
Resolution: 1.33 Å
Organism: Azotobacter vinelandii
Chains: 4
Atoms: 18,215
Mol. weight: 233.92 kDa
Ligands: CA, CLF, CMO, H2S
Released: 24 Mar 2021

Explore 7JRF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7JRF contains 118 α-helices and 76 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 27 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	22-29	8
β-strand	32-34	3	1
α-helix	42-44	3
α-helix	51-53	3
β-strand	58	1	2
α-helix	63-64	2
α-helix	65-72	8
β-strand	79-83	5	3
α-helix	87-91	5
β-strand	98	1	4
β-strand	104	1	5
β-strand	108	1	5
β-strand	114-115	2	3
α-helix	120-125	6
α-helix	128-141	14
β-strand	148-152	5	3
α-helix	155-159	5
α-helix	163-174	12
β-strand	178-181	4	3
α-helix	191-205	15
β-strand	222-228	7	6
β-strand	231	1	4
α-helix	236-244	9
β-strand	248-254	7	6
α-helix	259-264	6
α-helix	265-267	3
β-strand	270-273	4	6
α-helix	276-290	15
β-strand	294-296	3	6
α-helix	301-313	13
α-helix	318-346	29
β-strand	350-353	4	1
β-strand	355	1	1
α-helix	359-362	4
α-helix	364-368	5
β-strand	373-379	7	1
α-helix	384-393	10
α-helix	395	1
β-strand	399-402	4	1
β-strand	405	1	2
α-helix	406-416	11
β-strand	420-423	4	1
α-helix	425-433	9
β-strand	438-440	3	1
α-helix	444-446	3
α-helix	452-467	16
α-helix	470-474	5

Chain B: 32 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	7
β-strand	7	1	7
α-helix	11-14	4
α-helix	18-27	10
α-helix	28-32	5
α-helix	34-36	3
α-helix	37-46	10
α-helix	50-57	8
β-strand	63-64	2	3
α-helix	71-80	10
β-strand	82	1	8
β-strand	85-90	6	9
α-helix	93-107	15
β-strand	114-115	2	9
α-helix	122-125	4
α-helix	128-142	15
β-strand	146-151	6	9
α-helix	153-158	6
α-helix	162-171	10
β-strand	183	1	9
α-helix	193-209	17
α-helix	210-215	6
β-strand	224-227	4	10
α-helix	234-246	13
β-strand	251-253	3	10
β-strand	276	1	8
α-helix	278-283	6
α-helix	284-286	3
β-strand	289-292	4	10
α-helix	295-297	3
α-helix	299-304	6
α-helix	305-309	5
β-strand	320	1	11
α-helix	321-336	16
α-helix	338-341	4
α-helix	342-362	21
β-strand	366-370	5	12
α-helix	373-385	13
β-strand	389-395	7	12
α-helix	400-411	12
α-helix	414-416	3
β-strand	420-423	4	12
α-helix	427-436	10
β-strand	441-444	4	12
α-helix	448-458	11
α-helix	460-462	3
β-strand	466-468	3	12
α-helix	479-481	3
α-helix	486-508	23
α-helix	516-518	3

Chain C: 28 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	22-29	8
β-strand	32-34	3	13
α-helix	42-44	3
α-helix	51-53	3
β-strand	58	1	14
α-helix	63-64	2
α-helix	65-72	8
β-strand	79-83	5	15
α-helix	87-91	5
β-strand	98	1	16
β-strand	104	1	17
β-strand	108	1	17
β-strand	114-115	2	15
α-helix	120-125	6
α-helix	128-141	14
β-strand	148-152	5	15
α-helix	155-159	5
α-helix	163-174	12
β-strand	178-181	4	15
α-helix	191-202	12
α-helix	203-207	5
β-strand	222-228	7	18
β-strand	231	1	16
α-helix	236-244	9
β-strand	248-254	7	18
α-helix	259-264	6
α-helix	265-267	3
β-strand	270-273	4	18
α-helix	276-290	15
β-strand	294-296	3	18
α-helix	301-313	13
α-helix	318-346	29
β-strand	350-353	4	13
β-strand	355	1	13
α-helix	359-362	4
α-helix	364-368	5
β-strand	373-379	7	13
α-helix	384-393	10
α-helix	395	1
β-strand	399-402	4	13
β-strand	405	1	14
α-helix	406-416	11
β-strand	420-423	4	13
α-helix	425-433	9
β-strand	438-440	3	13
α-helix	444-446	3
α-helix	452-467	16
α-helix	470-473	4

Chain D: 31 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	18-27	10
α-helix	28-32	5
α-helix	34-36	3
α-helix	37-47	11
α-helix	50-57	8
β-strand	63-64	2	15
α-helix	71-80	10
β-strand	82	1	19
β-strand	85-90	6	20
α-helix	93-107	15
β-strand	114-115	2	20
α-helix	122-125	4
α-helix	128-142	15
β-strand	146-151	6	20
α-helix	153-158	6
α-helix	162-171	10
β-strand	183	1	20
α-helix	193-209	17
α-helix	210-215	6
β-strand	224-227	4	21
α-helix	234-246	13
β-strand	251-253	3	21
β-strand	276	1	19
α-helix	278-283	6
α-helix	284-286	3
β-strand	289-292	4	21
α-helix	295-297	3
α-helix	299-307	9
β-strand	320	1	22
α-helix	321-336	16
α-helix	338-341	4
α-helix	342-362	21
β-strand	366-370	5	23
α-helix	373-385	13
β-strand	389-395	7	23
α-helix	400-411	12
α-helix	414-416	3
β-strand	420-423	4	23
α-helix	427-436	10
β-strand	441-444	4	23
α-helix	448-458	11
α-helix	460-462	3
β-strand	466-468	3	23
α-helix	479-481	3
α-helix	486-508	23
α-helix	516-518	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nitrogenase molybdenum-iron protein alpha chain	A, C	protein	492	Azotobacter vinelandii	P07328 (AlphaFold model)
Nitrogenase molybdenum-iron protein beta chain	B, D	protein	523	Azotobacter vinelandii	P07329 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7JRF_1 Nitrogenase molybdenum-iron protein alpha chain (chains A, C)
MTGMSREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQPGLMTIR
GCAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQE
KDIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVP
VRCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRI
LLEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFF
GPTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRP
RHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDL
IGSGIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWE
ASEGAEKVAASA

Sequence of entity 2 (B, D), FASTA

>7JRF_2 Nitrogenase molybdenum-iron protein beta chain (chains B, D)
MSQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQRE
ALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTE
DAAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFP
VPFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVI
KRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEK
TKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHT
WLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNAT
VYIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLH
RSTTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
CLF	FE(8)-S(7) cluster	Fe8 S7	2
CMO	Carbon monoxide	C O	4
H2S	Hydrosulfuric acid	H2 S	2
ICE	iron-sulfur-molybdenum cluster with interstitial carbon	C Fe7 Mo S8	2
HCA	3-hydroxy-3-carboxy-adipic acid	C7 H10 O7	2
MG	Magnesium ion	Mg	2

Water and common crystallization additives (IMD) are not listed.

Primary citation

Structural Characterization of Two CO Molecules Bound to the Nitrogenase Active Site. Buscagan, T.M., Perez, K.A., Maggiolo, A.O. et al. Angew Chem Int Ed Engl (2021) 60:5704-5707. DOI 10.1002/anie.202015751 · PubMed

Other PDB entries of the same protein (UniProt P07328 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3U7Q 1.0 Å, A. vinelandii nitrogenase MoFe protein at atomic resolution
1M1N 1.16 Å, Nitrogenase MoFe protein from Azotobacter vinelandii
6O7M 1.4 Å, Nitrogenase MoFeP mutant F99Y from Azotobacter vinelandii in the indigo carmine oxidized…
4TKU 1.43 Å, Reactivated Nitrogenase MoFe-protein from A. vinelandii
4TKV 1.5 Å, CO-bound Nitrogenase MoFe-protein from A. vinelandii
5BVH 1.53 Å, CO-bound form of Selenium incorporated nitrogenase MoFe-protein (Av1-Se-CO) from A.…
8P8G 1.55 Å, Nitrogenase MoFe protein from A. vinelandii beta double mutant D353G/D357G
5BVG 1.6 Å, Selenium incorporated nitrogenase MoFe-protein (Av1-Se2B) from A. vinelandii
6OP3 1.6 Å, Selenium incorporated FeMo-cofactor of nitrogenase from Azotobacter vinelandii with low…
7MCI 1.65 Å, MoFe protein from Azotobacter vinelandii with a sulfur-replenished cofactor
6BBL 1.68 Å, Crystal structure of the a-96Gln MoFe protein variant in the presence of the substrate…
6O7P 1.7 Å, Nitrogenase MoFeP mutant F99Y from Azotobacter vinelandii in the dithionite reduced state

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