2qdy

Crystal Structure of Fe-type NHase from Rhodococcus erythropolis AJ270

Method: X-RAY DIFFRACTION

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

Nitrile hydratase subunit alpha

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Nitrile hydratase subunit beta × 1 （P13449） FE (III) ION × 1 CHLORIDE ION × 4 MAGNESIUM ION × 3 GLYCEROL × 6 2-METHYLPROPAN-1-AMINE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Nitrile hydratase subunit beta × 2 （P13449） FE (III) ION × 2 CHLORIDE ION × 8 MAGNESIUM ION × 6 GLYCEROL × 12 2-METHYLPROPAN-1-AMINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NHAA_RHOER
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–207； UniProt 1–207

Nitrile hydratase subunit beta

OrganismNot specified

UniProt P13449

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Nitrile hydratase subunit alpha × 1 （P13448） FE (III) ION × 1 CHLORIDE ION × 4 MAGNESIUM ION × 3 GLYCEROL × 6 2-METHYLPROPAN-1-AMINE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Nitrile hydratase subunit alpha × 2 （P13448） FE (III) ION × 2 CHLORIDE ION × 8 MAGNESIUM ION × 6 GLYCEROL × 12 2-METHYLPROPAN-1-AMINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NHAB_RHOER
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–212； UniProt 1–212

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	2qdy
Deposition date deposition_date	2007-06-22
Structure title title	Crystal Structure of Fe-type NHase from Rhodococcus erythropolis AJ270
Keywords keywords	nitrile hydratase, post translation, LYASE; LYASE
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.

2qdy__assembly_1__model_1

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

Download this curve (.dat)

2qdy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qdy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.20 Å
Rg (electron density)	20.99 Å
Total Rg	21.88 Å
Atom count	3248
Residues	406
Excluded volume	57592 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qdy__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2qdy__assembly_2__model_1`	tetrameric （4）	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 (8)

Entity 1 Entity 1 polymer

Description description	Nitrile hydratase subunit alpha
Molecular weight formula_weight	23081.1 kDa
EC 编号 ec_number	4.2.1.84
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3972

MSVTIDHTTENAAPAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLCSCTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQVPTV

Entity 2 Entity 2 polymer

Description description	Nitrile hydratase subunit beta
Molecular weight formula_weight	23514.3 kDa
EC 编号 ec_number	4.2.1.84
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDGVHDLAGVQGFGKVPHTVNADIGPTFHAEWEHLPYSLMFAGVAELGAFSVDEVRYVVERMEPRHYMMTPYYERYVIGVATLMVEKGILTQDELESLAGGPFPLSRPSESEGRPAPVETTTFEVGQRVRVRDEYVPGHIRMPAYCRGRVGTISHRTTEKWPFPDAIGHGRNDAGEEPTYHVKFAAEELFGSDTDGGSVVVDLFEGYLEPAA

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	2-METHYLPROPAN-1-AMINE
Molecular weight formula_weight	73.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	585

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2qdya_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.149 — Nitrile hydratase alpha chain
Superfamily Superfamily superfamily	d.149.1 — Nitrile hydratase alpha chain
Family Family family	d.149.1.1 — Nitrile hydratase alpha chain

Domain ID domain_id	d2qdyb_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.4 — Electron transport accessory proteins
Family Family family	b.34.4.4 — Nitrile hydratase beta chain

CATH v4.4 (3 domains)

Domain ID domain_id	2qdyA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	330 — Nitrile Hydratase; Chain A
Homologous superfamily homologous superfamily	10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma

Domain ID domain_id	2qdyB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	20 — Nitrile hydratase, beta subunit

Domain ID domain_id	2qdyB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	114.064 Å
Unit-cell length b length_b	60.068 Å
Unit-cell length c length_c	81.761 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	125.15 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	35.300 Å
R factor r_factor	0.1310
R_work r_work	0.1290
R_free r_free	0.1570

Crystal Structure of Fe-type NHase from Rhodococcus erythropolis AJ270

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

Nitrile hydratase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Nitrile hydratase subunit beta

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

2qdy__assembly_1__model_1

2qdy__assembly_1__model_1 | I(q)

2qdy__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal Structure of Fe-type NHase from Rhodococcus erythropolis AJ270

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

Nitrile hydratase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nitrile hydratase subunit beta

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

2qdy__assembly_1__model_1

2qdy__assembly_1__model_1 | I(q)

2qdy__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)