SAXSdb — 2pfw

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

Cupin 2, conserved barrel domain protein

Shewanella frigidimarina

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q07YH2_SHEFN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–116； UniProt 1–115 Author chain B； PDBConstruct 2–116； UniProt 1–115

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	2pfw
Deposition date deposition_date	2007-04-05
Structure title title	CRYSTAL STRUCTURE OF A RMLC-LIKE CUPIN (SFRI_3105) FROM SHEWANELLA FRIGIDIMARINA NCIMB 400 AT 1.90 A RESOLUTION
Keywords keywords	;CUPIN DOMAIN, CUPIN 2 CONSERVED BARREL DOMAIN PROTEIN, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, 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.

2pfw__assembly_1__model_1

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

Download this curve (.dat)

2pfw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2pfw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.45 Å
Rg (electron density)	16.29 Å
Total Rg	17.20 Å
Atom count	1763
Residues	217
Excluded volume	31098 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2pfw__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Cupin 2, conserved barrel domain protein
Molecular weight formula_weight	12882.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1880

GMQQSEHFSFGEQTEIEDIGGGLKRQMLGFNHELMAVKIWFDKGAEGYVHAHRHSQVSYVVEGEFHVNVDGVIKVLTAGDSFFVPPHVDHGAVCPTGGILIDTFSPAREDFVEGLS

Source Source

Source organism organism	Shewanella frigidimarina
NCBI taxonomy ID ncbi_taxonomy_id	318167
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	111

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2pfwA00
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	2pfwB00
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	58.500 Å
Unit-cell length b length_b	73.140 Å
Unit-cell length c length_c	73.130 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	29.248 Å
R factor r_factor	0.1930
R_work r_work	0.1890
R_free r_free	0.2560

CRYSTAL STRUCTURE OF A RMLC-LIKE CUPIN (SFRI_3105) FROM SHEWANELLA FRIGIDIMARINA NCIMB 400 AT 1.90 A RESOLUTION

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

Cupin 2, conserved barrel domain 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

2pfw__assembly_1__model_1

2pfw__assembly_1__model_1 | I(q)

2pfw__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF A RMLC-LIKE CUPIN (SFRI_3105) FROM SHEWANELLA FRIGIDIMARINA NCIMB 400 AT 1.90 A RESOLUTION

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

Cupin 2, conserved barrel domain 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

2pfw__assembly_1__model_1

2pfw__assembly_1__model_1 | I(q)

2pfw__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)