SAXSdb — 1w3v

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

ISOPENICILLIN N SYNTHETASE

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FE (II) ION × 1 N~6~-METHYL-6-OXO-L-LYSINE - 2-[(3-MERCAPTOBUTANOYL)OXY]-3-METHYLBUTANOIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IPNS_EMENI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–331； UniProt 1–331

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	1w3v
Deposition date deposition_date	2004-07-20
Structure title title	Isopenicillin N synthase d-(L-a-aminoadipoyl)-(3R)-methyl-L-cysteine D-a-hydroxyisovaleryl ester complex (anaerobic)
Keywords keywords	SYNTHASE, ANTIBIOTIC BIOSYNTHESIS, B-LACTAM ANTIBIOTIC, IRON, OXIDOREDUCTASE, OXYGENASE, PENICILLIN BIOSYNTHESIS; SYNTHASE
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.

1w3v__assembly_1__model_1

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

Download this curve (.dat)

1w3v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1w3v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.53 Å
Rg (electron density)	19.21 Å
Total Rg	20.13 Å
Atom count	2631
Residues	329
Excluded volume	46374 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1w3v__assembly_1__model_1`	monomeric （1）	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	ISOPENICILLIN N SYNTHETASE
Molecular weight formula_weight	37563.8 kDa
EC 编号 ec_number	1.21.3.1
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	2918

MGSVSKANVPKIDVSPLFGDDQAAKMRVAQQIDAASRDTGFFYAVNHGINVQRLSQKTKEFHMSITPEEKWDLAIRAYNKEHQDQVRAGYYLSIPGKKAVESFCYLNPNFTPDHPRIQAKTPTHEVNVWPDETKHPGFQDFAEQYYWDVFGLSSALLKGYALALGKEENFFARHFKPDDTLASVVLIRYPYLDPYPEAAIKTAADGTKLSFEWHEDVSLITVLYQSNVQNLQVETAAGYQDIEADDTGYLINCGSYMAHLTNNYYKAPIHRVKWVNAERQSLPFFVNLGYDSVIDPFDPREPNGKSDREPLSYGDYLQNGLVSLINKNGQT

Source Source

Source organism organism	Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)
Common name common_name	Aspergillus nidulans
NCBI taxonomy ID ncbi_taxonomy_id	227321
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	N~6~-METHYL-6-OXO-L-LYSINE - 2-[(3-MERCAPTOBUTANOYL)OXY]-3-METHYLBUTANOIC ACID
Molecular weight formula_weight	378.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	284

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1w3va_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.1 — Penicillin synthase-like

CATH v4.4 (1 domains)

Domain ID domain_id	1w3vA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	330 — B-lactam Antibiotic, Isopenicillin N Synthase; Chain

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Unit-cell length a length_a	46.994 Å
Unit-cell length b length_b	71.030 Å
Unit-cell length c length_c	100.916 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	57.740 Å
R factor r_factor	0.1620
R_work r_work	0.1610
R_free r_free	0.1750

Isopenicillin N synthase d-(L-a-aminoadipoyl)-(3R)-methyl-L-cysteine D-a-hydroxyisovaleryl ester complex (anaerobic)

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

ISOPENICILLIN N SYNTHETASE

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

1w3v__assembly_1__model_1

1w3v__assembly_1__model_1 | I(q)

1w3v__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Isopenicillin N synthase d-(L-a-aminoadipoyl)-(3R)-methyl-L-cysteine D-a-hydroxyisovaleryl ester complex (anaerobic)

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

ISOPENICILLIN N SYNTHETASE

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

1w3v__assembly_1__model_1

1w3v__assembly_1__model_1 | I(q)

1w3v__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)