SAXSdb — 6nvw

▼

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

Penicillin G acylase

Bacillus megaterium

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 × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAC_BACME
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–210； UniProt 25–234 Author chain B； PDBConstruct 1–537； UniProt 266–802

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6nvw
Deposition date deposition_date	2019-02-05
Structure title title	Crystal structure of penicillin G acylase from Bacillus megaterium
Keywords keywords	penicillin, acylase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6nvw__assembly_1__model_1

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

Download this curve (.dat)

6nvw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nvw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.59 Å
Rg (electron density)	26.57 Å
Total Rg	27.53 Å
Atom count	11302
Residues	719
Excluded volume	102460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nvw__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Penicillin G acylase
Molecular weight formula_weight	24452.5 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	11613

GEDKNEGVKVVRDNFGVPHLYAKNKKDLYEAYGYVMAKDRLFQLEMFRRGNEGTVSEIFGEDYLSKDEQSRRDGYSNKEIKKMIDGLDRQPKELIAKFAEGISRYVNEALKDPDDKLSKEFHEYQFLPQKWTSTDVVRVYMVSMTYFMDNHQELKNAEILAKLEHEYGTEVSRKMFDDLVWKNDPSAPTSIVSEGKPKRDSSSQSLQILS

Source Source

Source organism organism	Bacillus megaterium
NCBI taxonomy ID ncbi_taxonomy_id	1404
Host organism host_organism	Bacillus megaterium

Entity 2 Entity 2 polymer

Description description	Penicillin G acylase
Molecular weight formula_weight	61475.9 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	B

SNAAIVGSEKSATGNALLFSGPQVGFVAPGFLYEVGLHAPGFDMEGSGFIGYPFIMFGANNHFALSATAGYGNVTDIFEEKLNAKNSSQYLYKGKWRDMEKRKESFTVKGDNGEKKTVEKIYYRTVHGPVISRDETNKVAYSKSWSFRGTEAQSMSAYMKANWAKNLKEFENAASEYTMSLNWYYADKKGDIAYYHVGRYPVRNSKIDERIPTPGTGEYEWKGFIPFKENPHVINPKNGYVVNWNNKPSKEWVNGEYSFYWGEDNRVQQYINGMEARGKVTLEDINEINYTASFAQLRANLFKQLLIDVLDKNKSTNGNYIYLIEKLEEWNNLKEDENKDGYYDAGIAAFFDEWWNNLHDKLFMDELGDFYGITKEITDHRYGASLAYKILNKESTNYKWVNVDQEKIIMESTNEVLAKLQSEKGLKAEKWRMPIKTMTFGEKSLIGIPHGYGSMTPIIEMNRGSENHYIEMTPTGPSGFNITPPGQIGFVKKDGTISDHYDDQLVMFAEWKFKPYLFNKKDINKAAKNVSALNMSK

Source Source

Source organism organism	Bacillus megaterium
NCBI taxonomy ID ncbi_taxonomy_id	1404
Host organism host_organism	Bacillus megaterium

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	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	256

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6nvwB01
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	6nvwB02
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

▶

Unit-cell length a length_a	58.238 Å
Unit-cell length b length_b	77.961 Å
Unit-cell length c length_c	84.086 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.67 °
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	2.203 Å
Low-resolution limit resolution_low	46.032 Å
R factor r_factor	0.2175
R_work r_work	0.2146
R_free r_free	0.2747

Crystal structure of penicillin G acylase from Bacillus megaterium

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

Penicillin G acylase

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

6nvw__assembly_1__model_1

6nvw__assembly_1__model_1 | I(q)

6nvw__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of penicillin G acylase from Bacillus megaterium

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

Penicillin G acylase

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

6nvw__assembly_1__model_1

6nvw__assembly_1__model_1 | I(q)

6nvw__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)