SAXSdb — 2qyv

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

Xaa-His dipeptidase

Haemophilus somnus 129PT

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 SULFATE ION × 18 GLYCEROL × 17 ISOPROPYL ALCOHOL × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q0I1B9_HAES1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–487； UniProt 1–486 Author chain B； PDBConstruct 2–487； UniProt 1–486

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	2qyv
Deposition date deposition_date	2007-08-15
Structure title title	Crystal structure of putative Xaa-His dipeptidase (YP_718209.1) from Haemophilus somnus 129PT at 2.11 A resolution
Keywords keywords	;YP_718209.1, putative Xaa-His dipeptidase, 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.

2qyv__assembly_1__model_1

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

Download this curve (.dat)

2qyv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qyv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.18 Å
Rg (electron density)	32.66 Å
Total Rg	33.08 Å
Atom count	7420
Residues	928
Excluded volume	132330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qyv__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 (6)

Entity 1 Entity 1 polymer

Description description	Xaa-His dipeptidase
Molecular weight formula_weight	54119.2 kDa
EC 编号 ec_number	3.4.13.20
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	7920

GMSDLQSLQPKLLWQWFDQICAIPHPSYKEEQLAQFIINWAKTKGFFAERDEVGNVLIRKPATVGMENRKPVVLQAHLDMVPQANEGTNHNFDQDPILPYIDGDWVKAKGTTLGADNGIGMASALAVLESNDIAHPELEVLLTMTEERGMEGAIGLRPNWLRSEILINTDTEENGEIYIGCAGGENADLELPIEYQVNNFEHCYQVVLKGLRGGHSGVDIHTGRANAIKVLLRFLAELQQNQPHFDFTLANIRGGSIRNAIPRESVATLVFNGDITVLQSAVQKFADVIKAELALTEPNLIFTLEKVEKPQQVFSSQCTKNIIHCLNVLPNGVVRNSDVIENVVETSLSIGVLKTEDNFVRSTMLVRSLIESGKSYVASLLKSLASLAQGNINLSGDYPGWEPQSHSDILDLTKTIYAQVLGTDPEIKVIHAGLECGLLKKIYPTIDMVSIGPTIRNAHSPDEKVHIPAVETYWKVLTGILAHIPSR

Source Source

Source organism organism	Haemophilus somnus 129PT
NCBI taxonomy ID ncbi_taxonomy_id	205914
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 5 Entity 5 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	466

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2qyvA01
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	2qyvB01
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	173.922 Å
Unit-cell length b length_b	84.293 Å
Unit-cell length c length_c	123.204 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.110 Å
Low-resolution limit resolution_low	47.836 Å
R factor r_factor	0.2210
R_work r_work	0.2200
R_free r_free	0.2440

Crystal structure of putative Xaa-His dipeptidase (YP_718209.1) from Haemophilus somnus 129PT at 2.11 A resolution

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

Xaa-His dipeptidase

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

2qyv__assembly_1__model_1

2qyv__assembly_1__model_1 | I(q)

2qyv__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of putative Xaa-His dipeptidase (YP_718209.1) from Haemophilus somnus 129PT at 2.11 A resolution

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

Xaa-His dipeptidase

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

2qyv__assembly_1__model_1

2qyv__assembly_1__model_1 | I(q)

2qyv__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)