SAXSdb — 7w8m

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

Nitrile hydratase

Pseudonocardia thermophila DSM 43832

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cobalt-containing nitrile hydratase subunit beta × 2 （Q7SID3） COBALT (II) ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A1M6Q338_PSETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–205； UniProt 1–205

Cobalt-containing nitrile hydratase subunit beta

Pseudonocardia thermophila

UniProt Q7SID3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Nitrile hydratase × 2 （A0A1M6Q338） COBALT (II) ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NHAB_PSETH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–233； UniProt 1–233

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	7w8m
Deposition date deposition_date	2021-12-08
Structure title title	Crystal structure of Co-type nitrile hydratase mutant from Pseudomonas thermophila - A129R
Keywords keywords	hydratase, catalyze the hydration of nitriles to form amides, 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.

7w8m__assembly_1__model_1

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

Download this curve (.dat)

7w8m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7w8m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.06 Å
Rg (electron density)	29.35 Å
Total Rg	30.03 Å
Atom count	6948
Residues	858
Excluded volume	122880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7w8m__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Nitrile hydratase
Molecular weight formula_weight	23290.7 kDa
EC 编号 ec_number	4.2.1.84
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	3580

MTENILRKSDEEIQKEITARVKALESMLIEQGILTTSMIDRMAEIYENEVGPHLGAKVVVKAWTDPEFKKRLLADGTEACKELGIGGLQGEDMMWVENTDEVHHVVVCTLCSCYPWPVLGLPPNWFKEPQYRSRVVREPRQLLKEEFGFEVPPSKEIKVWDSSSEMRFVVLPQRPAGTDGWSEEELATLVTRESMIGVEPAKAVA

Source Source

Source organism organism	Pseudonocardia thermophila DSM 43832
NCBI taxonomy ID ncbi_taxonomy_id	1123026
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Cobalt-containing nitrile hydratase subunit beta
Molecular weight formula_weight	26669.8 kDa
EC 编号 ec_number	4.2.1.84
Mutation mutation	A129R
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MNGVYDVGGTDGLGPINRPADEPVFRAEWEKVAFAMFPATFRAGFMGLDEFRFGIEQMNPAEYLESPYYWHWIRTYIHHGVRTGKIDLEELERRTQYYRENPDAPLPEHEQKPELIEFVNQAVYGGLPRSREVDRPPKFKEGDVVRFSTASPKGHARRARYVRGKTGTVVKHHGAYIYPDTAGNGLGECPEHLYTVRFTAQELWGPEGDPNSSVYYDCWEPYIELVDTKAAAA

Source Source

Source organism organism	Pseudonocardia thermophila
NCBI taxonomy ID ncbi_taxonomy_id	1848
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 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	103

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Unit-cell length a length_a	65.517 Å
Unit-cell length b length_b	65.517 Å
Unit-cell length c length_c	183.754 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	22.370 Å
R factor r_factor	0.1805
R_work r_work	0.1774
R_free r_free	0.2402

Crystal structure of Co-type nitrile hydratase mutant from Pseudomonas thermophila - A129R

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

Nitrile hydratase

State in the Current Structure

Other States of the Same Protein in the Database

Cobalt-containing 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

7w8m__assembly_1__model_1

7w8m__assembly_1__model_1 | I(q)

7w8m__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

7. Citations (2)

Crystal structure of Co-type nitrile hydratase mutant from Pseudomonas thermophila - A129R

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

Nitrile hydratase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cobalt-containing 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

7w8m__assembly_1__model_1

7w8m__assembly_1__model_1 | I(q)

7w8m__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

7. Citations (2)