SAXSdb — 3cpx

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

Aminopeptidase, M42 family

Cytophaga hutchinsonii ATCC 33406

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	FE (III) ION × 6 1,2-ETHANEDIOL × 12 CHLORIDE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q11Z05_CYTH3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–321； UniProt 1–302 Author chain B； PDBConstruct 20–321； UniProt 1–302 Author chain C； PDBConstruct 20–321； 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	3cpx
Deposition date deposition_date	2008-04-01
Structure title title	Crystal structure of putative M42 glutamyl aminopeptidase (YP_676701.1) from Cytophaga hutchinsonii ATCC 33406 at 2.39 A resolution
Keywords keywords	;YP_676701.1, Putative M42 Glutamyl Aminopeptidase, 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.

3cpx__assembly_1__model_1

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

Download this curve (.dat)

3cpx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cpx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.13 Å
Rg (electron density)	28.22 Å
Total Rg	28.93 Å
Atom count	7388
Residues	908
Excluded volume	131390 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cpx__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 (5)

Entity 1 Entity 1 polymer

Description description	Aminopeptidase, M42 family
Molecular weight formula_weight	37006.6 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	7728

MGSDKIHHHHHHENLYFQGMQLLKELCSIHAPSGNEEPLKDFILEYIRSNAGSWSYQPVIYADNDLQDCIVLVFGNPRTAVFAHMDSIGFTVSYNNHLHPIGSPSAKEGYRLVGKDSNGDIEGVLKIVDEEWMLETDRLIDRGTEVTFKPDFREEGDFILTPYLDDRLGVWTALELAKTLEHGIIAFTCWEEHGGGSVAYLARWIYETFHVKQSLICDITWVTEGVEAGKGVAISMRDRMIPRKKYVNRIIELARQTDIPFQLEVEGAGASDGRELQLSPYPWDWCFIGAPEKDAHTPNECVHKKDIESMVGLYKYLMEKL

Source Source

Source organism organism	Cytophaga hutchinsonii ATCC 33406
NCBI taxonomy ID ncbi_taxonomy_id	269798
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	322

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3cpxA01
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	3cpxA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	40 — Peptidase M42, domain 2

Domain ID domain_id	3cpxB01
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	3cpxB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	40 — Peptidase M42, domain 2

Domain ID domain_id	3cpxC01
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	3cpxC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	40 — Peptidase M42, domain 2

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Unit-cell length a length_a	83.840 Å
Unit-cell length b length_b	83.840 Å
Unit-cell length c length_c	682.310 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 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.390 Å
Low-resolution limit resolution_low	29.656 Å
R factor r_factor	0.1890
R_work r_work	0.1870
R_free r_free	0.2230

Crystal structure of putative M42 glutamyl aminopeptidase (YP_676701.1) from Cytophaga hutchinsonii ATCC 33406 at 2.39 A resolution

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

Aminopeptidase, M42 family

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

3cpx__assembly_1__model_1

3cpx__assembly_1__model_1 | I(q)

3cpx__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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of putative M42 glutamyl aminopeptidase (YP_676701.1) from Cytophaga hutchinsonii ATCC 33406 at 2.39 A resolution

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

Aminopeptidase, M42 family

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

3cpx__assembly_1__model_1

3cpx__assembly_1__model_1 | I(q)

3cpx__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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)