SAXSdb — 1gm8

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

PENICILLIN G ACYLASE ALPHA SUBUNIT

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 1 N-[(2S,4S,6R)-2-(DIHYDROXYMETHYL)-4-HYDROXY-3,3-DIMETHYL-7-OXO-4LAMBDA~4~-THIA-1-AZABICYCLO[3.2.0]HEPT-6-YL]-2-PHENYLAC ETAMIDE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAC_ECOLI
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–209； UniProt 27–235 Author chain B； PDBConstruct 1–557； UniProt 290–846

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	1gm8
Deposition date deposition_date	2001-09-11
Structure title title	Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism
Keywords keywords	ANTIBIOTIC RESISTANCE, 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.

1gm8__assembly_1__model_1

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

Download this curve (.dat)

1gm8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1gm8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.67 Å
Rg (electron density)	26.54 Å
Total Rg	27.46 Å
Atom count	6099
Residues	764
Excluded volume	107700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1gm8__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 (5)

Entity 1 Entity 1 polymer

Description description	PENICILLIN G ACYLASE ALPHA SUBUNIT
Molecular weight formula_weight	23838.8 kDa
EC 编号 ec_number	3.5.1.11
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6754

EQSSSEIKIVRDEYGMPHIYANDTWHLFYGYGYVVAQDRLFQMEMARRSTQGTVAEVLGKDFVKFDKDIRRNYWPDAIRAQIAALSPEDMSILQGYADGMNAWIDKVNTNPETLLPKQFNTFGFTPKRWEPFDVAMIFVGTMANRFSDSTSEIDNLALLTALKDKYGVSQGMAVFNQLKWLVNPSAPTTIAVQESNYPLKFNQQNSQTA

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	PENICILLIN G ACYLASE BETA SUBUNIT
Molecular weight formula_weight	62386.5 kDa
EC 编号 ec_number	3.5.1.11
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SNMWVIGKSKAQDAKAIMVNGPQFGWYAPAYTYGIGLHGAGYDVTGNTPFAYPGLVFGHNGVISWGSTAGFGDDVDIFAERLSAEKPGYYLHNGKWVKMLSREETITVKNGQAETFTVWRTVHGNILQTDQTTQTAYAKSRAWDGKEVASLLAWTHQMKAKNWQEWTQQAAKQALTINWYYADVNGNIGYVHTGAYPDRQSGHDPRLPVPGTGKWDWKGLLPFEMNPKVYNPQSGYIANWANSPQKDYPASDLFAFLWGGADRVTEIDRLLEQKPRLTADQAWDVIRQTSRQDLNLRLFLPTLQAATSGLTQSDPRRQLVETLTRWDGINLLNDDGKTWQQPGSAILNVWLTSMLKRTVVAAVPMPFDKWYSASGYETTQDGPTGSLNISVGAKILYEAVQGDKSPIPQAVDLFAGKPQQEVVLAALEDTWETLSKRYGNNVSNWKTPAMALTFRANNFFGVPQAAAEETRHQAEYQNRGTENDMIVFSPTTSDRPVLAWDVVAPGQSGFIAPDGTVDKHYEDQLKMYENFGRKSLWLTKQDVEAHKESQEVLHVQR

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	N-[(2S,4S,6R)-2-(DIHYDROXYMETHYL)-4-HYDROXY-3,3-DIMETHYL-7-OXO-4LAMBDA~4~-THIA-1-AZABICYCLO[3.2.0]HEPT-6-YL]-2-PHENYLAC ETAMIDE
Molecular weight formula_weight	352.4 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	644

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1gm8.1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.2 — Penicillin acylase, catalytic domain

CATH v4.4 (5 domains)

Domain ID domain_id	1gm8A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	439 — Penicillin Amidohydrolase; domain 1
Homologous superfamily homologous superfamily	10 — Penicillin Amidohydrolase, domain 1

Domain ID domain_id	1gm8A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	1gm8B01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1gm8B02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	120 — Penicillin G acylase, beta-roll domain
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region

Domain ID domain_id	1gm8B03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1400 — Penicillin amidase (Acylase) alpha subunit, N-terminal domain
Homologous superfamily homologous superfamily	10 — Aminohydrolase, alpha-helical knob region

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Unit-cell length a length_a	51.200 Å
Unit-cell length b length_b	131.200 Å
Unit-cell length c length_c	63.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.1620
R_free r_free	0.2340

Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism

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

PENICILLIN G ACYLASE ALPHA SUBUNIT

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

1gm8__assembly_1__model_1

1gm8__assembly_1__model_1 | I(q)

1gm8__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

CATH v4.4 (5 domains)

7. Citations (3)

Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism

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

PENICILLIN G ACYLASE ALPHA SUBUNIT

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

1gm8__assembly_1__model_1

1gm8__assembly_1__model_1 | I(q)

1gm8__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

CATH v4.4 (5 domains)

7. Citations (3)