9rll

Sub-atomic resolution (0.95 A) XFEL structure of as-isolated copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography (SF-ROX)

Method: X-RAY DIFFRACTION

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

Copper-containing nitrite reductase

Achromobacter cycloclastes

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	COPPER (II) ION × 6 SULFATE ION × 21 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIR_ACHCY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–334； UniProt 45–378

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	9rll
Deposition date deposition_date	2025-06-16
Structure title title	Sub-atomic resolution (0.95 A) XFEL structure of as-isolated copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography (SF-ROX)
Keywords keywords	Copper-containing nitrite reductase, AcNiR, SF-ROX, as-isolated, sub-atomic resolution, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

9rll__assembly_1__model_1

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

Download this curve (.dat)

9rll__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9rll__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.70 Å
Rg (electron density)	27.50 Å
Total Rg	28.46 Å
Atom count	15276
Residues	996
Excluded volume	137690 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9rll__assembly_1__model_1`	trimeric （3）	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	Copper-containing nitrite reductase
Molecular weight formula_weight	36620.3 kDa
EC 编号 ec_number	1.7.2.1
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	5834

VDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYQDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM

Source Source

Source organism organism	Achromobacter cycloclastes
NCBI taxonomy ID ncbi_taxonomy_id	223
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	501

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Unit-cell length a length_a	95.250 Å
Unit-cell length b length_b	95.250 Å
Unit-cell length c length_c	95.250 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	12

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	0.950 Å
Low-resolution limit resolution_low	16.844 Å
R factor r_factor	—
R_work r_work	0.1344
R_free r_free	0.1605

Sub-atomic resolution (0.95 A) XFEL structure of as-isolated copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography (SF-ROX)

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

Copper-containing nitrite reductase

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

9rll__assembly_1__model_1

9rll__assembly_1__model_1 | I(q)

9rll__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

7. Citations (1)

Sub-atomic resolution (0.95 A) XFEL structure of as-isolated copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography (SF-ROX)

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

Copper-containing nitrite reductase

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

9rll__assembly_1__model_1

9rll__assembly_1__model_1 | I(q)

9rll__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

7. Citations (1)