1mio

X-RAY CRYSTAL STRUCTURE OF THE NITROGENASE MOLYBDENUM-IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM AT 3.0 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION

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

NITROGENASE MOLYBDENUM IRON PROTEIN (ALPHA CHAIN)

Clostridium pasteurianum

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 （P11347） CALCIUM ION × 2 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 FE-MO-S CLUSTER × 2 FE-S CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIFD_CLOPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–533； UniProt 1–533 Author chain C； PDBConstruct 1–533； UniProt 1–533

NITROGENASE MOLYBDENUM IRON PROTEIN (BETA CHAIN)

Clostridium pasteurianum

UniProt P11347

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 （P00467） CALCIUM ION × 2 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 FE-MO-S CLUSTER × 2 FE-S CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIFK_CLOPA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–458； UniProt 1–458 Author chain D； PDBConstruct 1–458； UniProt 1–458

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	1mio
Deposition date deposition_date	1993-03-24
Structure title title	X-RAY CRYSTAL STRUCTURE OF THE NITROGENASE MOLYBDENUM-IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM AT 3.0 ANGSTROMS RESOLUTION
Keywords keywords	MOLYBDENUM-IRON PROTEIN; MOLYBDENUM-IRON PROTEIN
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.

1mio__assembly_1__model_1

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

Download this curve (.dat)

1mio__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1mio__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.63 Å
Rg (electron density)	39.12 Å
Total Rg	39.45 Å
Atom count	15269
Residues	1964
Excluded volume	273230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1mio__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 (6)

Entity 1 Entity 1 polymer

Description description	NITROGENASE MOLYBDENUM IRON PROTEIN (ALPHA CHAIN)
Molecular weight formula_weight	59071.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	15269

SENLKDEILEKYIPKTKKTRSGHIVIKTEETPNPEIVANTRTVPGIITARGCAYAGCKGVVMGPIKDMVHITHGPIGCSFYTWGGRRFKSKPENGTGLNFNEYVFSTDMQESDIVFGGVNKLKDAIHEAYEMFHPAAIGVYATCPVGLIGDDILAVAATASKEIGIPVHAFSCEGYKGVSQSAGHHIANNTVMTDIIGKGNKEQKKYSINVLGEYNIGGDAWEMDRVLEKIGYHVNATLTGDATYEKVQNADKADLNLVQCHRSINYIAEMMETKYGIPWIKCNFIGVDGIVETLRDMAKCFDDPELTKRTEEVIAEEIAAIQDDLDYFKEKLQGKTACLYVGGSRSHTYMNMLKSFGVDSLVAGFEFAHRDDYEGREVIPTIKIDADSKNIPEITVTPDEQKYRVVIPEDKVEELKKAGVPLSSYGGMMKEMHDGTILIDDMNHHDMEVVLEKLKPDMFFAGIKEKFVIQKGGVLSKQLHSYDYNGPYAGFRGVVNFGHELVNGIYTPAWKMITPPWKKASSESKVVVGGEA

Source Source

Source organism organism	Clostridium pasteurianum
NCBI taxonomy ID ncbi_taxonomy_id	1501

Entity 2 Entity 2 polymer

Description description	NITROGENASE MOLYBDENUM IRON PROTEIN (BETA CHAIN)
Molecular weight formula_weight	50175.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MLDATPKEIVERKALRINPAKTCQPVGAMYAALGIHNCLPHSHGSQGCCSYHRTVLSRHFKEPAMASTSSFTEGASVFGGGSNIKTAVKNIFSLYNPDIIAVHTTCLSETLGDDLPTYISQMEDAGSIPEGKLVIHTNTPSYVGSHVTGFANMVQGIVNYLSENTGAKNGKINVIPGFVGPADMREIKRLFEAMDIPYIMFPDTSGVLDGPTTGEYKMYPEGGTKIEDLKDTGNSDLTLSLGSYASDLGAKTLEKKCKVPFKTLRTPIGVSATDEFIMALSEATGKEVPASIEEERGQLIDLMIDAQQYLQGKKVALLGDPDEIIALSKFIIELGAIPKYVVTGTPGMKFQKEIDAMLAEAGIEGSKVKVEGDFFDVHQWIKNEGVDLLISNTYGKFIAREENIPFVRFGFPIMDRYGHYYNPKVGYKGAIRLVEEITNVILDKIERECTEEDFEVVR

Source Source

Source organism organism	Clostridium pasteurianum
NCBI taxonomy ID ncbi_taxonomy_id	1501

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 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 5 Entity 5 non-polymer

Description description	FE-MO-S CLUSTER
Molecular weight formula_weight	775.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	FE-S CLUSTER
Molecular weight formula_weight	703.3 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1mioa_
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	d1miob_
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	d1mioc_
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	d1miod_
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	1mioA01
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	1mioA02
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	1mioA03
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	1mioB01
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	1mioB02
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	1mioB03
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	1mioB04
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	1mioC01
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	1mioC02
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	1mioC03
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	1mioD01
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	1mioD02
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	1mioD03
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	1mioD04
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	69.960 Å
Unit-cell length b length_b	151.300 Å
Unit-cell length c length_c	121.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.40 °
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	3.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1800
R_work r_work	0.1800
R_free r_free	—

X-RAY CRYSTAL STRUCTURE OF THE NITROGENASE MOLYBDENUM-IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM AT 3.0 ANGSTROMS RESOLUTION

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

1mio__assembly_1__model_1

1mio__assembly_1__model_1 | I(q)

1mio__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (4 domains)

CATH v4.4 (14 domains)

7. Citations (3)

X-RAY CRYSTAL STRUCTURE OF THE NITROGENASE MOLYBDENUM-IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM AT 3.0 ANGSTROMS RESOLUTION

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

1mio__assembly_1__model_1

1mio__assembly_1__model_1 | I(q)

1mio__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (4 domains)

CATH v4.4 (14 domains)

7. Citations (3)