SAXSdb — 4fut

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

Malonyl CoA synthetase

Rhodopseudomonas palustris

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	GLYCEROL × 6 MAGNESIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6ND88_RHOPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–503； UniProt 1–503

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	4fut
Deposition date deposition_date	2012-06-28
Structure title title	Crystal structure of ATP bound MatB from Rhodopseudomonas palustris
Keywords keywords	ANL Superfamily, methymalonyl-CoA synthetase, CoA, methylmalonate, malonate, LIGASE; LIGASE
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.

4fut__assembly_1__model_1

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

Download this curve (.dat)

4fut__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4fut__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.16 Å
Rg (electron density)	23.22 Å
Total Rg	24.09 Å
Atom count	3955
Residues	475
Excluded volume	70985 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4fut__assembly_1__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	Malonyl CoA synthetase
Molecular weight formula_weight	55221.3 kDa
EC 编号 ec_number	6.2.1.-
Mutation mutation	K488A
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	4604

MNANLFARLFDKLDDPHKLAIETAAGDKISYAELVARAGRVANVLVARGLQVGDRVAAQTEKSVEALVLYLATVRAGGVYLPLNTAYTLHELDYFITDAEPKIVVCDPSKRDGIAAIAAKVGATVETLGPDGRGSLTDAAAGASEAFATIDRGADDLAAILYTSGTTGRSKGAMLSHDNLASNSLTLVDYWRFTPDDVLIHALPIYHTHGLFVASNVTLFARGSMIFLPKFDPDKILDLMARATVLMGVPTFYTRLLQSPRLTKETTGHMRLFISGSAPLLADTHREWSAKTGHAVLERYGMTETNMNTSNPYDGDRVPGAVGPALPGVSARVTDPETGKELPRGDIGMIEVKGPNVFKGYWRMPEKTKSEFRDDGFFITGDLGKIDERGYVHILGRGKDLVITGGFNVYPKEIESEIDAMPGVVESAVIGVPHADFGEGVTAVVVRDKGATIDEAQVLHGLDGQLAKFKMPKKVIFVDDLPRNTMGAVQKNVLRETYKDIYK

Source Source

Source organism organism	Rhodopseudomonas palustris
NCBI taxonomy ID ncbi_taxonomy_id	258594
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	609

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4futa_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.23 — Acetyl-CoA synthetase-like
Superfamily Superfamily superfamily	e.23.1 — Acetyl-CoA synthetase-like
Family Family family	e.23.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	4futA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12780 — ANL, N-terminal domain

Domain ID domain_id	4futA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	30 — ANL, C-terminal domain

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Unit-cell length a length_a	173.140 Å
Unit-cell length b length_b	173.140 Å
Unit-cell length c length_c	47.739 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	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	24.991 Å
R factor r_factor	0.1598
R_work r_work	0.1578
R_free r_free	0.1962

Crystal structure of ATP bound MatB from Rhodopseudomonas palustris

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

Malonyl CoA synthetase

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

4fut__assembly_1__model_1

4fut__assembly_1__model_1 | I(q)

4fut__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of ATP bound MatB from Rhodopseudomonas palustris

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

Malonyl CoA synthetase

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

4fut__assembly_1__model_1

4fut__assembly_1__model_1 | I(q)

4fut__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)