SAXSdb — 1nxj

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

Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	GLYOXYLIC ACID × 3 L(+)-TARTARIC ACID × 3 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	GLYOXYLIC ACID × 3 L(+)-TARTARIC ACID × 3 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	GLYOXYLIC ACID × 3 L(+)-TARTARIC ACID × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRAA_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 27–183； UniProt 1–157 Author chain B； PDBConstruct 27–183； UniProt 1–157 Author chain C； PDBConstruct 27–183； UniProt 1–157

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	1nxj
Deposition date deposition_date	2003-02-10
Structure title title	Structure of Rv3853 from Mycobacterium tuberculosis
Keywords keywords	;beta/beta/alpha domain, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, UNKNOWN FUNCTION ;; UNKNOWN FUNCTION
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.

1nxj__assembly_1__model_1

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

Download this curve (.dat)

1nxj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nxj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.07 Å
Rg (electron density)	23.21 Å
Total Rg	24.04 Å
Atom count	3447
Residues	468
Excluded volume	61002 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nxj__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1nxj__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1nxj__assembly_3__model_1`	trimeric （3）	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	Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase
Molecular weight formula_weight	19380.8 kDa
EC 编号 ec_number	2.1.-.-
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3705

MSYYHHHHHHDYDIPTTGNLYFQGAMVAISFRPTADLVDDIGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYOXYLIC ACID
Molecular weight formula_weight	74.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	L(+)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	276

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1nxja_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.7 — RraA-like
Family Family family	c.8.7.1 — RraA-like

Domain ID domain_id	d1nxjb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.7 — RraA-like
Family Family family	c.8.7.1 — RraA-like

Domain ID domain_id	d1nxjc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.7 — RraA-like
Family Family family	c.8.7.1 — RraA-like

CATH v4.4 (3 domains)

Domain ID domain_id	1nxjA00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	40 — Ribonuclease E inhibitor RraA/RraA-like

Domain ID domain_id	1nxjB00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	40 — Ribonuclease E inhibitor RraA/RraA-like

Domain ID domain_id	1nxjC00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	40 — Ribonuclease E inhibitor RraA/RraA-like

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Unit-cell length a length_a	102.462 Å
Unit-cell length b length_b	102.462 Å
Unit-cell length c length_c	117.494 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	18

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	24.610 Å
R factor r_factor	—
R_work r_work	0.1900
R_free r_free	0.2150

Structure of Rv3853 from Mycobacterium tuberculosis

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

Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase

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

1nxj__assembly_1__model_1

1nxj__assembly_1__model_1 | I(q)

1nxj__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Structure of Rv3853 from Mycobacterium tuberculosis

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

Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase

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

1nxj__assembly_1__model_1

1nxj__assembly_1__model_1 | I(q)

1nxj__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)