6rkd

Molybdenum storage protein under turnover conditions

Method: ELECTRON MICROSCOPY

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

Molybdenum storage protein subunit alpha

Azotobacter vinelandii (strain DJ / ATCC BAA-1303)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Molybdenum storage protein subunit beta × 6 （P84253） ADENOSINE-5'-TRIPHOSPHATE × 12 MAGNESIUM ION × 6 bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI) × 12 ;oxidanyl-[[2,2,4,4,4-pentakis($l^{1}-oxidanyl)-1-(oxidanylmolybdenio)-1$l^{3},3-dioxa-2$l^{5},4$l^{5}-dimolybdacyclobut-2-yl]oxy]molybdenum ; × 12 MOLYBDATE ION × 42 MO(VI)(=O)(OH)2 CLUSTER × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MOSA_AZOVD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 1–276 Author chain C； PDBConstruct 1–276； UniProt 1–276 Author chain E； PDBConstruct 1–276； UniProt 1–276 Author chain G； PDBConstruct 1–276； UniProt 1–276 Author chain I； PDBConstruct 1–276； UniProt 1–276 Author chain K； PDBConstruct 1–276； UniProt 1–276

Molybdenum storage protein subunit beta

Azotobacter vinelandii (strain DJ / ATCC BAA-1303)

UniProt P84253

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Molybdenum storage protein subunit alpha × 6 （P84308） ADENOSINE-5'-TRIPHOSPHATE × 12 MAGNESIUM ION × 6 bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI) × 12 ;oxidanyl-[[2,2,4,4,4-pentakis($l^{1}-oxidanyl)-1-(oxidanylmolybdenio)-1$l^{3},3-dioxa-2$l^{5},4$l^{5}-dimolybdacyclobut-2-yl]oxy]molybdenum ; × 12 MOLYBDATE ION × 42 MO(VI)(=O)(OH)2 CLUSTER × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MOSB_AZOVD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–270； UniProt 1–270 Author chain D； PDBConstruct 1–270； UniProt 1–270 Author chain F； PDBConstruct 1–270； UniProt 1–270 Author chain H； PDBConstruct 1–270； UniProt 1–270 Author chain J； PDBConstruct 1–270； UniProt 1–270 Author chain L； PDBConstruct 1–270； UniProt 1–270

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	6rkd
Deposition date deposition_date	2019-04-30
Structure title title	Molybdenum storage protein under turnover conditions
Keywords keywords	molybdenum storage protein, ATPase, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

6rkd__assembly_1__model_1

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

Download this curve (.dat)

6rkd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6rkd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.92 Å
Rg (electron density)	44.20 Å
Total Rg	43.54 Å
Atom count	25266
Residues	3234
Excluded volume	449530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6rkd__assembly_1__model_1`	dodecameric （12）	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 (8)

Entity 1 Entity 1 polymer

Description description	Molybdenum storage protein subunit alpha
Molecular weight formula_weight	29376.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	25290

MTDTTNSIKHVISPLARQTLQDRDLTRPVAGKRPIRLLPWLQVVKIGGRVMDRGADAILPLVEELRKLLPEHRLLILTGAGVRARHVFSVGLDLGLPVGSLAPLAASEAGQNGHILAAMLASEGVSYVEHPTVADQLAIHLSATRAVVGSAFPPYHHHEFPGSRIPPHRADTGAFLLADAFGAAGLTIVENVDGIYTADPNGPDRGQARFLPETSATDLAKSEGPLPVDRALLDVMATARHIERVQVVNGLVPGRLTAALRGEHVGTLIRTGVRPA

Source Source

Source organism organism	Azotobacter vinelandii (strain DJ / ATCC BAA-1303)
NCBI taxonomy ID ncbi_taxonomy_id	322710
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Molybdenum storage protein subunit beta
Molecular weight formula_weight	28378.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

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

MANSTAELEELLMQRSLTDPQLQAAAAAAADFRILPDATVIKIGGQSVIDRGRAAVYPLVDEIVAARKNHKLLIGTGAGTRARHLYSIAAGLGLPAGVLAQLGSSVADQNAAMLGQLLAKHGIPVVGGAGLSAVPLSLAEVNAVVFSGMPPYKLWMRPAAEGVIPPYRTDAGCFLLAEQFGCKQMIFVKDEDGLYTANPKTSKDATFIPRISVDEMKAKGLHDSILEFPVLDLLQSAQHVREVQVVNGLVPGNLTRALAGEHVGTIITAS

Source Source

Source organism organism	Azotobacter vinelandii (strain DJ / ATCC BAA-1303)
NCBI taxonomy ID ncbi_taxonomy_id	322710
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI)
Molecular weight formula_weight	1215.5 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 6 Entity 6 non-polymer

Description description	;oxidanyl-[[2,2,4,4,4-pentakis($l^{1}-oxidanyl)-1-(oxidanylmolybdenio)-1$l^{3},3-dioxa-2$l^{5},4$l^{5}-dimolybdacyclobut-2-yl]oxy]molybdenum ;
Molecular weight formula_weight	545.8 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 7 Entity 7 non-polymer

Description description	MOLYBDATE ION
Molecular weight formula_weight	159.9 kDa
Source method src_method	syn
Copy count entity_count	42

Entity 8 Entity 8 non-polymer

Description description	MO(VI)(=O)(OH)2 CLUSTER
Molecular weight formula_weight	146.0 kDa
Source method src_method	syn
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	6rkdA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	6rkdB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	6rkdC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	6rkdD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	6rkdE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	6rkdF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	6rkdG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	6rkdH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	6rkdI00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	6rkdJ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	6rkdK00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	6rkdL00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

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

Resolution resolution	3.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	137558

Molybdenum storage protein under turnover conditions

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

Molybdenum storage protein subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Molybdenum storage protein subunit beta

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

6rkd__assembly_1__model_1

6rkd__assembly_1__model_1 | I(q)

6rkd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

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

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Molybdenum storage protein under turnover conditions

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

Molybdenum storage protein subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Molybdenum storage protein subunit beta

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

6rkd__assembly_1__model_1

6rkd__assembly_1__model_1 | I(q)

6rkd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

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

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)