SAXSdb — 9q1a

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

D-lysine 5,6-aminomutase beta subunit

Caldanaerobacter subterraneus subsp. tengcongensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	D-lysine 5,6-aminomutase alpha subunit × 2 （Q8RBT3） COBALAMIN × 2 5'-DEOXYADENOSINE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8RBT2_CALS4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–257； UniProt 12–268 Author chain B； PDBConstruct 1–257； UniProt 12–268

D-lysine 5,6-aminomutase alpha subunit

Caldanaerobacter subterraneus subsp. tengcongensis

UniProt Q8RBT3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	D-lysine 5,6-aminomutase beta subunit × 2 （Q8RBT2） COBALAMIN × 2 5'-DEOXYADENOSINE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8RBT3_CALS4
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–517； UniProt 2–518 Author chain D； PDBConstruct 1–517； UniProt 2–518

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	9q1a
Deposition date deposition_date	2025-08-13
Structure title title	Open state of lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
Keywords keywords	lysine 5, 6-aminomutase, cobalamin, vitamin B12, pyridoxal phosphate, radical, ISOMERASE; ISOMERASE
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.

9q1a__assembly_1__model_1

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

Download this curve (.dat)

9q1a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9q1a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.64 Å
Rg (electron density)	39.70 Å
Total Rg	39.97 Å
Atom count	24813
Residues	1545
Excluded volume	221690 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9q1a__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 (4)

Entity 1 Entity 1 polymer

Description description	D-lysine 5,6-aminomutase beta subunit
Molecular weight formula_weight	28612.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	24813

QYDTTLDLTRVKPYGDTMNDGKVQLSFTLPVPDGAKAVEAAKQLAKKMGLENPMVVYHAPLDKNFTFFIIYGSLIHTVDYTSIQVQELEIKAMSMEETNEYIKKHIGRKVVVVGATTGTDAHTVGLDAIMNMKGYAGHYGLERYEMIEAYNLGSQVPNEEFVKKAIEVGADALLVSQTVTQKDAHIKNLTHLVELLEAEGIRDKVLLICGGPRITHELAKELGYDAGFGPGTFADHVATFIVTEMVKRKIPGLKGYK

Source Source

Source organism organism	Caldanaerobacter subterraneus subsp. tengcongensis
NCBI taxonomy ID ncbi_taxonomy_id	119072
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	D-lysine 5,6-aminomutase alpha subunit
Molecular weight formula_weight	57943.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

RESKLNLDWELVDKAREAARNIVKDTQKFIDAHTTVSVERTVCRLLGIDGVNDLGVPLPNVVVDHIKSKGNLSLGAATYIGNAMIYTGLSPQEIAERVAKGELDLTSIPMADLFEIKLAVQDIAIKTVEKIRENRRKREEFLKKYGDKEGPLLYVIVATGNIYEDVVQAQAAARQGADVIAVIRATAQSLLDYVPYGPTTEGFGGTYATQENFRIMRKALDEVSEELGRYIRLCNYASGLCMPEIAAMGALERLDVMLNDALYGILFRDINMKRTMVDQFFSRVINGFAGIIINTGEDNYLTTADAYEKAHTVLASQLINEQFALIAGIPEEQMGLGHAFEMNPDLRNGFLYELAQAQMVREIFPKAPLKYMPPTKYMTGNIFKGHVQDAMFNVVTIMTKQRIHLLGMLTEAIHTPFMSDRALSIESAKYIFNNMADIADEIYFKEGGIIQRRANEVLKKAYELLKEIEQEGLFKALEQGKFADIKRPIDGGKGLEGVVEKDPNYFNPFIDLMLRGD

Source Source

Source organism organism	Caldanaerobacter subterraneus subsp. tengcongensis
NCBI taxonomy ID ncbi_taxonomy_id	119072
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	COBALAMIN
Molecular weight formula_weight	1330.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	5'-DEOXYADENOSINE
Molecular weight formula_weight	251.2 kDa
Source method src_method	syn
Copy count entity_count	2

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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	—

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

Resolution resolution	2.83 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1482472

Open state of lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis

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

D-lysine 5,6-aminomutase beta subunit

State in the Current Structure

Other States of the Same Protein in the Database

D-lysine 5,6-aminomutase alpha subunit

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

9q1a__assembly_1__model_1

9q1a__assembly_1__model_1 | I(q)

9q1a__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 (4)

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

7. Citations (1)

Open state of lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis

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

D-lysine 5,6-aminomutase beta subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

D-lysine 5,6-aminomutase alpha subunit

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

9q1a__assembly_1__model_1

9q1a__assembly_1__model_1 | I(q)

9q1a__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 (4)

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

7. Citations (1)