2qmi

Structure of the octameric penicillin-binding protein homologue from Pyrococcus abyssi

Method: X-RAY DIFFRACTION

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

Pbp related beta-lactamase

Pyrococcus abyssi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	LUTETIUM (III) ION × 17 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9V2D6_PYRAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–447； UniProt 1–447 Author chain B； PDBConstruct 1–447； UniProt 1–447 Author chain C； PDBConstruct 1–447； UniProt 1–447 Author chain D； PDBConstruct 1–447； UniProt 1–447 Author chain E； PDBConstruct 1–447； UniProt 1–447 Author chain F； PDBConstruct 1–447； UniProt 1–447 Author chain G； PDBConstruct 1–447； UniProt 1–447 Author chain H； PDBConstruct 1–447； UniProt 1–447

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	2qmi
Deposition date deposition_date	2007-07-16
Structure title title	Structure of the octameric penicillin-binding protein homologue from Pyrococcus abyssi
Keywords keywords	PAB87, OCTAMER, LU-HPDO3A, PBP, ARCHAEA, 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.

2qmi__assembly_1__model_1

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

Download this curve (.dat)

2qmi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qmi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.32 Å
Rg (electron density)	47.25 Å
Total Rg	48.12 Å
Atom count	28514
Residues	3573
Excluded volume	517880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qmi__assembly_1__model_1`	octameric （8）	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	Pbp related beta-lactamase
Molecular weight formula_weight	50503.4 kDa
EC 编号 ec_number	3.5.2.6
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	30882

MDVGKLESFIVEKMAERKVPGISISIIKDGDVVYAKGFGYRNVEARLPSTPETIYGIGSITKSFTALAIMKLVEEGGLSLDDPVEKFVNIKLRPFGEPVTVHHLLTHSSGIPSLGYAEAFIDGMVGGDNWLPVSTPEETIAFARDMEKWAVAKPGERFFYLNTGYVLLGKIIEKVSGVSYEEYIKKKILEPLGMNRSYFFKEEVEKDKDVAMGYILDKEGRLVPQPFPYGITADGGLLSSVLDLAKYLKMYIERDESIVSKEYIEKMETSYIKVPWEIFGGEGYGYGLIIYPNFLGEKLVGHSGSVGMYTGYIGYIPEKKIGVAVLENSSGYPPSYIAMYALALLLGKNPEKELPFIYRERILKKVEGRYMGYKGTIKFEVKVDGDVVYLRALGRAFTYTIPLFPEVLEEDFIKCYTLSNGRKMYAEFYIKDNKVDLIFERYRLIKS

Source Source

Source organism organism	Pyrococcus abyssi
NCBI taxonomy ID ncbi_taxonomy_id	29292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	LUTETIUM (III) ION
Molecular weight formula_weight	175.0 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 3 Entity 3 non-polymer

Description description	10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID
Molecular weight formula_weight	404.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2368

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	2qmiA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2qmiA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	210 — Pab87 octamerisation domain

Domain ID domain_id	2qmiB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2qmiB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	210 — Pab87 octamerisation domain

Domain ID domain_id	2qmiC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2qmiC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	210 — Pab87 octamerisation domain

Domain ID domain_id	2qmiD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2qmiD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	210 — Pab87 octamerisation domain

Domain ID domain_id	2qmiE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2qmiE02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	210 — Pab87 octamerisation domain

Domain ID domain_id	2qmiF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2qmiF02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	210 — Pab87 octamerisation domain

Domain ID domain_id	2qmiG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2qmiG02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	210 — Pab87 octamerisation domain

Domain ID domain_id	2qmiH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2qmiH02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	210 — Pab87 octamerisation domain

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Unit-cell length a length_a	100.940 Å
Unit-cell length b length_b	105.630 Å
Unit-cell length c length_c	112.920 Å
Unit-cell angle α angle_alpha	72.17 °
Unit-cell angle β angle_beta	66.51 °
Unit-cell angle γ angle_gamma	81.39 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2410

Structure of the octameric penicillin-binding protein homologue from Pyrococcus abyssi

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

Pbp related beta-lactamase

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

2qmi__assembly_1__model_1

2qmi__assembly_1__model_1 | I(q)

2qmi__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) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Structure of the octameric penicillin-binding protein homologue from Pyrococcus abyssi

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

Pbp related beta-lactamase

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

2qmi__assembly_1__model_1

2qmi__assembly_1__model_1 | I(q)

2qmi__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) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)