SAXSdb — 7z3d

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

Ribonucleoside-diphosphate reductase subunit beta

Bacillus cereus ATCC 14579

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Protein NrdI × 2 （B0YPL1） MANGANESE (II) ION × 4 UNKNOWN ATOM OR ION × 2 FLAVIN MONONUCLEOTIDE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q81G55_BACCR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–322； UniProt 1–322

Protein NrdI

Bacillus cereus ATCC 14579

UniProt B0YPL1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Ribonucleoside-diphosphate reductase subunit beta × 2 （Q81G55） MANGANESE (II) ION × 4 UNKNOWN ATOM OR ION × 2 FLAVIN MONONUCLEOTIDE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B0YPL1_BACCE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–119； UniProt 1–119

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	7z3d
Deposition date deposition_date	2022-03-02
Structure title title	XFEL structure of Class Ib ribonucleotide reductase dimanganese(II) NrdF in complex with oxidized NrdI from Bacillus cereus
Keywords keywords	;Ribonucleotide reductase R2b, Class Ib RNR, Flavoprotein, Metalloenzyme, OXIDOREDUCTASE, ferritin-like superfamily, dimanganese cofactor, XFEL ;; 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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7z3d__assembly_1__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Ribonucleoside-diphosphate reductase subunit beta
Molecular weight formula_weight	37053.0 kDa
EC 编号 ec_number	1.17.4.1
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	3655

MRAVNWNKKEDDFSLMFWKQNIAQFWTEEEIAVSSDKNTWVQLSKEEQIAYKRVLGGLTLLDTKQGGEGMPLVLVHLENLQAKSVLAFMGAMEEVHAKSYSHIFTTLATEEEIDDIFDWVDNHPLLEKKAGIITSYYRRLLKPEVTKKELYMAMVASVFLESYLFYSGFFYPLYLAGQGKLTASGEIINLIIRDESIHGVFVGILAQQIFAELSAEEQQEVQKETQELLMELYEIEMAYTEEIYTSIGLVEDVNRFVRYNANKGLMNLGLEPKFEEEEINPIVLNGLRTDTKNHDFFSVKGNGYVKATNVEKLADDDFVFNF

Source Source

Source organism organism	Bacillus cereus ATCC 14579
NCBI taxonomy ID ncbi_taxonomy_id	226900
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Protein NrdI
Molecular weight formula_weight	13539.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MLVAYDSMTGNVKRFIHKLNMPAVQIDEDLVIDEDFILITYTTGFGNVPERVLDFLERNNEKLKGVSASGNRNWGDMFGASADKISTKYEVPIVSKFELSGTNNDVEYFKERVREIATH

Source Source

Source organism organism	Bacillus cereus ATCC 14579
NCBI taxonomy ID ncbi_taxonomy_id	226900
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	UNKNOWN ATOM OR ION
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	159

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Unit-cell length a length_a	61.438 Å
Unit-cell length b length_b	125.634 Å
Unit-cell length c length_c	144.997 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	orthorhombic

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	24.170 Å
R factor r_factor	0.1609
R_work r_work	0.1591
R_free r_free	0.1956

XFEL structure of Class Ib ribonucleotide reductase dimanganese(II) NrdF in complex with oxidized NrdI from Bacillus cereus

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

Ribonucleoside-diphosphate reductase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Protein NrdI

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

XFEL structure of Class Ib ribonucleotide reductase dimanganese(II) NrdF in complex with oxidized NrdI from Bacillus cereus

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

Ribonucleoside-diphosphate reductase 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

Protein NrdI

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)