6o7p

Nitrogenase MoFeP mutant F99Y from Azotobacter vinelandii in the dithionite reduced state

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nitrogenase molybdenum-iron protein alpha chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Nitrogenase molybdenum-iron protein beta chain × 2 （P07329） 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 iron-sulfur-molybdenum cluster with interstitial carbon × 2 FE(8)-S(7) CLUSTER × 2 FE (III) ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIFD_AZOVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–492； UniProt 1–492 Author chain C； PDBConstruct 1–492； UniProt 1–492

Nitrogenase molybdenum-iron protein beta chain

OrganismNot specified

UniProt P07329

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Nitrogenase molybdenum-iron protein alpha chain × 2 （P07328） 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 iron-sulfur-molybdenum cluster with interstitial carbon × 2 FE(8)-S(7) CLUSTER × 2 FE (III) ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIFK_AZOVI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–523； UniProt 1–523 Author chain D； PDBConstruct 1–523； UniProt 1–523

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6o7p
Deposition date deposition_date	2019-03-08
Structure title title	Nitrogenase MoFeP mutant F99Y from Azotobacter vinelandii in the dithionite reduced state
Keywords keywords	Nitrogenase, F99Y, MoFeP, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6o7p__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6o7p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6o7p__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	38.34 Å
Rg (electron density)	37.69 Å
Total Rg	38.09 Å
Atom count	31425
Residues	1998
Excluded volume	284290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6o7p__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Nitrogenase molybdenum-iron protein alpha chain
Molecular weight formula_weight	55363.0 kDa
EC 编号 ec_number	1.18.6.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	34126

MTGMSREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQPGLMTIRGCAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWEASEGAEKVAASA

Entity 2 Entity 2 polymer

Description description	Nitrogenase molybdenum-iron protein beta chain
Molecular weight formula_weight	59551.9 kDa
EC 编号 ec_number	1.18.6.1
Mutation mutation	F99Y
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MSQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYYRSYFNRHFREPVSCVSDSMTEDAAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPVPFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKTKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR

Entity 3 Entity 3 non-polymer

Description description	3-HYDROXY-3-CARBOXY-ADIPIC ACID
Molecular weight formula_weight	206.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	iron-sulfur-molybdenum cluster with interstitial carbon
Molecular weight formula_weight	787.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	FE(8)-S(7) CLUSTER
Molecular weight formula_weight	671.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2529

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6o7pa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.92 — Chelatase-like
Superfamily Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
Family Family family	c.92.2.3 — Nitrogenase iron-molybdenum protein

Domain ID domain_id	d6o7pb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.92 — Chelatase-like
Superfamily Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
Family Family family	c.92.2.3 — Nitrogenase iron-molybdenum protein

Domain ID domain_id	d6o7pc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.92 — Chelatase-like
Superfamily Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
Family Family family	c.92.2.3 — Nitrogenase iron-molybdenum protein

Domain ID domain_id	d6o7pd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.92 — Chelatase-like
Superfamily Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
Family Family family	c.92.2.3 — Nitrogenase iron-molybdenum protein

CATH v4.4 (14 domains)

Domain ID domain_id	6o7pA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	6o7pA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	6o7pA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	6o7pB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	6o7pB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	6o7pB03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	89 — Nitrogenase Molybdenum-iron Protein, subunit B; domain 4
Homologous superfamily homologous superfamily	10 — Nitrogenase Molybdenum-iron Protein, subunit B, domain 4

Domain ID domain_id	6o7pB04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	6o7pC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	6o7pC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	6o7pC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	6o7pD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	6o7pD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	6o7pD03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	89 — Nitrogenase Molybdenum-iron Protein, subunit B; domain 4
Homologous superfamily homologous superfamily	10 — Nitrogenase Molybdenum-iron Protein, subunit B, domain 4

Domain ID domain_id	6o7pD04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

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Unit-cell length a length_a	76.847 Å
Unit-cell length b length_b	128.439 Å
Unit-cell length c length_c	107.707 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	46.652 Å
R factor r_factor	0.1711
R_work r_work	0.1677
R_free r_free	0.2013

Nitrogenase MoFeP mutant F99Y from Azotobacter vinelandii in the dithionite reduced state

1. Protein Identity and Related Structures Protein Identity & Related Structures

Nitrogenase molybdenum-iron protein alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Nitrogenase molybdenum-iron protein beta chain

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6o7p__assembly_1__model_1

6o7p__assembly_1__model_1 | I(q)

6o7p__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (4 domains)

CATH v4.4 (14 domains)

7. Citations (1)

Nitrogenase MoFeP mutant F99Y from Azotobacter vinelandii in the dithionite reduced state

1. Protein Identity and Related Structures Protein Identity & Related Structures

Nitrogenase molybdenum-iron protein alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nitrogenase molybdenum-iron protein beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6o7p__assembly_1__model_1

6o7p__assembly_1__model_1 | I(q)

6o7p__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (4 domains)

CATH v4.4 (14 domains)

7. Citations (1)