SAXSdb — 2vqa

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

SLL1358 PROTEIN

SYNECHOCYSTIS SP.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	MANGANESE (II) ION × 6 ACETATE ION × 8 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P73510_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–361； UniProt 35–394 Author chain B； PDBConstruct 2–361； UniProt 35–394 Author chain C； PDBConstruct 2–361； UniProt 35–394

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	2vqa
Deposition date deposition_date	2008-03-12
Structure title title	Protein-folding location can regulate Mn versus Cu- or Zn-binding. Crystal Structure of MncA.
Keywords keywords	PERIPLASMIC BINDING PROTEIN, METAL-BINDING PROTEIN, MN2+, CUPIN, BI-CUPIN, OXALATE DECARBOXYLASE, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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.

2vqa__assembly_1__model_1

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

Download this curve (.dat)

2vqa__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vqa__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.17 Å
Rg (electron density)	32.33 Å
Total Rg	33.15 Å
Atom count	8274
Residues	1066
Excluded volume	146870 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vqa__assembly_1__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	SLL1358 PROTEIN
Molecular weight formula_weight	39517.2 kDa
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	8306

MQSEQWRSLSNVVWGKDLPAFTYAFSKTPLVLYDGGTTKQVGTYNFPVSKGMAGVYMSLEPGAIRELHWHANAAEWAYVMEGRTRITLTSPEGKVEIADVDKGGLWYFPRGWGHSIEGIGPDTAKFLLVFNDGTFSEGATFSVTDWLSHTPIAWVEENLGWTAAQVAQLPKKQVYISSYGPASGPLASATPQGQTAKIEVPHTHNLLGQQPLVSLGGNELRLASAKEFPGSFNMTGALIHLEPGAMRQLHWHPNADEWQYVLDGEMDLTVFASEGKASVSRLQQGDVGYVPKGYGHAIRNSSQKPLDIVVVFNDGDYQSIDLSTWLASNPSSVLGNTFQISPELTKKLPVQDTIFSLPTQP

Source Source

Source organism organism	SYNECHOCYSTIS SP.
NCBI taxonomy ID ncbi_taxonomy_id	1148
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	6

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	32

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2vqaA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	2vqaA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	2vqaB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	2vqaB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	2vqaC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	2vqaC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

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Unit-cell length a length_a	236.190 Å
Unit-cell length b length_b	236.190 Å
Unit-cell length c length_c	134.041 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	36

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	58.320 Å
R factor r_factor	0.1930
R_work r_work	0.1910
R_free r_free	0.2330

Protein-folding location can regulate Mn versus Cu- or Zn-binding. Crystal Structure of MncA.

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

SLL1358 PROTEIN

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

2vqa__assembly_1__model_1

2vqa__assembly_1__model_1 | I(q)

2vqa__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

CATH v4.4 (6 domains)

7. Citations (1)

Protein-folding location can regulate Mn versus Cu- or Zn-binding. Crystal Structure of MncA.

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

SLL1358 PROTEIN

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

2vqa__assembly_1__model_1

2vqa__assembly_1__model_1 | I(q)

2vqa__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

CATH v4.4 (6 domains)

7. Citations (1)