SAXSdb — 7zcc

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

Uncharacterized protein YxbC

Bacillus subtilis subsp. subtilis str. 168

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 2 N-OXALYLGLYCINE × 2 GLYCEROL × 7 SULFATE ION × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 2 N-OXALYLGLYCINE × 2 GLYCEROL × 8 SULFATE ION × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YXBC_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–341； UniProt 1–330 Author chain B； PDBConstruct 12–341； UniProt 1–330 Author chain C； PDBConstruct 12–341； UniProt 1–330 Author chain D； PDBConstruct 12–341； UniProt 1–330

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	7zcc
Deposition date deposition_date	2022-03-27
Structure title title	yxBC from Bacillus subtilis in complex with Mn and N-oxalylglycine (NOG)
Keywords keywords	;OXIDOREDUCTASE, NON-HEME, IRON, 2-OXOGLUTARATE, DIOXYGENASE, OXYGENASE, JMJC, JMJC DOMAIN, JMJC HYDROXYLASE, JMJC DEMETHYLASE, KDMS, POST-TRANSLATIONAL MODIFICATIONS, PTM, HYDROXYLATION, HELIX-LOOP-HELIX-BETA, DSBH, FACIAL TRIAD ;; 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.

7zcc__assembly_1__model_1

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

Download this curve (.dat)

7zcc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7zcc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.30 Å
Rg (electron density)	26.06 Å
Total Rg	27.01 Å
Atom count	10082
Residues	651
Excluded volume	92031 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7zcc__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7zcc__assembly_2__model_1`	dimeric （2）	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	Uncharacterized protein YxbC
Molecular weight formula_weight	38823.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	21275

GSDKIHHHHHHMSAVTESVLESIISPVTMSEFLEEYWPVKPLVARGEVERFTSIPGFEKVRTLENVLAIYNNPVMVVGDAVIEESEGITDRFLVSPAEALEWYEKGAALEFDFTDLFIPQVRRWIEKLKAELRLPAGTSSKAIVYAAKNGGGFKAHFDAYTNLIFQIQGEKTWKLAKNENVSNPMQHYDLSEAPYYPDDLQSYWKGDPPKEDLPDAEIVNLTPGTMLYLPRGLWHSTKSDQATLALNITFGQPAWLDLMLAALRKKLISDNRFRELAVNHQSLHESSKSELNGYLESLIQTLSENAETLTPEQIFQSQDSDFDPYQSTQLVFRQLLTSYKF

Source Source

Source organism organism	Bacillus subtilis subsp. subtilis str. 168
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	N-OXALYLGLYCINE
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	807

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7zccA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	7zccB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	7zccC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	7zccD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

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Unit-cell length a length_a	109.733 Å
Unit-cell length b length_b	109.733 Å
Unit-cell length c length_c	192.191 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 31 1 2
Space-group number int_tables_number	151
Crystal system crystal_system	—

Resolution resolution	1.848 Å
Low-resolution limit resolution_low	47.647 Å
R factor r_factor	0.1671
R_work r_work	0.1654
R_free r_free	0.2002

yxBC from Bacillus subtilis in complex with Mn and N-oxalylglycine (NOG)

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

Uncharacterized protein YxbC

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

7zcc__assembly_1__model_1

7zcc__assembly_1__model_1 | I(q)

7zcc__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

yxBC from Bacillus subtilis in complex with Mn and N-oxalylglycine (NOG)

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

Uncharacterized protein YxbC

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

7zcc__assembly_1__model_1

7zcc__assembly_1__model_1 | I(q)

7zcc__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)