SAXSdb — 3b2y

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

Metallopeptidase containing co-catalytic metalloactive site

Shewanella denitrificans OS217

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	NICKEL (II) ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	NICKEL (II) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q12L70_SHEDO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–275； UniProt 1–274 Author chain B； PDBConstruct 2–275； UniProt 1–274

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	3b2y
Deposition date deposition_date	2007-10-19
Structure title title	CRYSTAL STRUCTURE OF a putative metallopeptidase (SDEN_2526) FROM SHEWANELLA DENITRIFICANS OS217 AT 1.74 A RESOLUTION
Keywords keywords	;METALLOPEPTIDASE CONTAINING CO-CATALYTIC METALLOACTIVE SITE, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, HYDROLASE ;; HYDROLASE
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.

3b2y__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3b2y__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3b2y__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.18 Å
Rg (electron density)	16.90 Å
Total Rg	17.96 Å
Atom count	2000
Residues	258
Excluded volume	35361 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3b2y__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3b2y__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Metallopeptidase containing co-catalytic metalloactive site
Molecular weight formula_weight	30579.7 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	4318

GMTSRSPFESFVWQSEIFNCQSNDIDAFYAQLAEEVNRLGLKKNTLGSVDSFAINLYQSASQRSDLPSLLISSGFHGEEAAGPWGMLHFLRGLQPALFERVNLSLLPLVNPTGFKAGHRFNRFGENPNRGFTLENGKPTPNEHTSLEGKLLLEHAQLLCAASRDGILTCHEDVLMNETYVYSFEPTQTPGRFSLGLRDALGQYFKLAKDGFIDECPVTDGVIFNHFDTSFEAFLVRSGAKLAACSETPGQEDFDRRVQANSAAMGQFIAHCAPIL

Source Source

Source organism organism	Shewanella denitrificans OS217
NCBI taxonomy ID ncbi_taxonomy_id	318161
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	230

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3b2yA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	3b2yB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

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Unit-cell length a length_a	43.715 Å
Unit-cell length b length_b	127.577 Å
Unit-cell length c length_c	49.303 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.740 Å
Low-resolution limit resolution_low	28.820 Å
R factor r_factor	0.1760
R_work r_work	0.1750
R_free r_free	0.2150

CRYSTAL STRUCTURE OF a putative metallopeptidase (SDEN_2526) FROM SHEWANELLA DENITRIFICANS OS217 AT 1.74 A RESOLUTION

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

Metallopeptidase containing co-catalytic metalloactive site

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

3b2y__assembly_2__model_1

3b2y__assembly_2__model_1 | I(q)

3b2y__assembly_2__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 putative metallopeptidase (SDEN_2526) FROM SHEWANELLA DENITRIFICANS OS217 AT 1.74 A RESOLUTION

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

Metallopeptidase containing co-catalytic metalloactive site

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

3b2y__assembly_2__model_1

3b2y__assembly_2__model_1 | I(q)

3b2y__assembly_2__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)