4wwb

High-resolution structure of the Ni-bound form of the Y135F mutant of C. metallidurans CnrXs

Method: X-RAY DIFFRACTION

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

Nickel and cobalt resistance protein CnrR

Ralstonia metallidurans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NICKEL (II) ION × 2 CHLORIDE ION × 4 CARBON DIOXIDE × 2 POTASSIUM ION × 2 FORMIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CNRR_RALME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–118； UniProt 31–148

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	4wwb
Deposition date deposition_date	2014-11-10
Structure title title	High-resolution structure of the Ni-bound form of the Y135F mutant of C. metallidurans CnrXs
Keywords keywords	Nickel sensor, metal binding protein; METAL BINDING PROTEIN
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.

4wwb__assembly_1__model_1

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

Download this curve (.dat)

4wwb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4wwb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.03 Å
Rg (electron density)	20.49 Å
Total Rg	21.26 Å
Atom count	3554
Residues	224
Excluded volume	31487 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4wwb__assembly_1__model_1`	dimeric （2）	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 (7)

Entity 1 Entity 1 polymer

Description description	Nickel and cobalt resistance protein CnrR
Molecular weight formula_weight	13295.9 kDa
Mutation mutation	Y135F
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	2291

SHRNEAGHGDLHEILHEAVPLDANEREILELKEDAFAQRRREIETRLRAANGKLADAIAKNPAWSPEVEAATQEVERAAGDLQRATLVHVFEMRAGLKPEHRPAFDRVLIDALRRGSQ

Source Source

Source organism organism	Ralstonia metallidurans
NCBI taxonomy ID ncbi_taxonomy_id	266264
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CARBON DIOXIDE
Molecular weight formula_weight	44.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	234

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Unit-cell length a length_a	32.401 Å
Unit-cell length b length_b	32.401 Å
Unit-cell length c length_c	195.331 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.110 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1090
R_work r_work	0.1083
R_free r_free	0.1237

High-resolution structure of the Ni-bound form of the Y135F mutant of C. metallidurans CnrXs

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

Nickel and cobalt resistance protein CnrR

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

4wwb__assembly_1__model_1

4wwb__assembly_1__model_1 | I(q)

4wwb__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

High-resolution structure of the Ni-bound form of the Y135F mutant of C. metallidurans CnrXs

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

Nickel and cobalt resistance protein CnrR

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

4wwb__assembly_1__model_1

4wwb__assembly_1__model_1 | I(q)

4wwb__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)