SAXSdb — 1kpi

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

CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 2

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CARBONATE ION × 1 SULFATE ION × 4 S-ADENOSYL-L-HOMOCYSTEINE × 1 DIDECYL-DIMETHYL-AMMONIUM × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CARBONATE ION × 2 SULFATE ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 2 DIDECYL-DIMETHYL-AMMONIUM × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CFA2_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–302； UniProt 1–302

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	1kpi
Deposition date deposition_date	2001-12-30
Structure title title	Crystal Structure of mycolic acid cyclopropane synthase CmaA2 complexed with SAH and DDDMAB
Keywords keywords	;mixed alpha beta fold, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, TRANSFERASE ;; TRANSFERASE
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.

1kpi__assembly_1__model_1

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

Download this curve (.dat)

1kpi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kpi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.63 Å
Rg (electron density)	18.28 Å
Total Rg	19.29 Å
Atom count	2436
Residues	291
Excluded volume	43174 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kpi__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1kpi__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	CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 2
Molecular weight formula_weight	34642.0 kDa
EC 编号 ec_number	2.1.1.79
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2498

MTSQGDTTSGTQLKPPVEAVRSHYDKSNEFFKLWLDPSMTYSCAYFERPDMTLEEAQYAKRKLALDKLNLEPGMTLLDIGCGWGSTMRHAVAEYDVNVIGLTLSENQYAHDKAMFDEVDSPRRKEVRIQGWEEFDEPVDRIVSLGAFEHFADGAGDAGFERYDTFFKKFYNLTPDDGRMLLHTITIPDKEEAQELGLTSPMSLLRFIKFILTEIFPGGRLPRISQVDYYSSNAGWKVERYHRIGANYVPTLNAWADALQAHKDEAIALKGQETCDIYMHYLRGCSDLFRDKYTDVCQFTLVK

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	DIDECYL-DIMETHYL-AMMONIUM
Molecular weight formula_weight	326.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	62

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1kpia_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.18 — Mycolic acid cyclopropane synthase

CATH v4.4 (1 domains)

Domain ID domain_id	1kpiA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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Unit-cell length a length_a	106.710 Å
Unit-cell length b length_b	106.710 Å
Unit-cell length c length_c	227.498 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	16

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	29.350 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2420

Crystal Structure of mycolic acid cyclopropane synthase CmaA2 complexed with SAH and DDDMAB

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

CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 2

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

1kpi__assembly_1__model_1

1kpi__assembly_1__model_1 | I(q)

1kpi__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structure of mycolic acid cyclopropane synthase CmaA2 complexed with SAH and DDDMAB

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

CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 2

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

1kpi__assembly_1__model_1

1kpi__assembly_1__model_1 | I(q)

1kpi__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)