1l1l

CRYSTAL STRUCTURE OF B-12 DEPENDENT (CLASS II) RIBONUCLEOTIDE REDUCTASE

Method: X-RAY DIFFRACTION

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

RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE

Lactobacillus leichmannii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RTPR_LACLE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–739； UniProt 1–739 Author chain B； PDBConstruct 1–739； UniProt 1–739 Author chain C； PDBConstruct 1–739； UniProt 1–739 Author chain D； PDBConstruct 1–739； UniProt 1–739

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	1l1l
Deposition date deposition_date	2002-02-18
Structure title title	CRYSTAL STRUCTURE OF B-12 DEPENDENT (CLASS II) RIBONUCLEOTIDE REDUCTASE
Keywords keywords	10-stranded alpha-beta barrel, central finger loop, 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.

1l1l__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1l1l__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1l1l__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	27.56 Å
Rg (electron density)	26.43 Å
Total Rg	27.25 Å
Atom count	5588
Residues	717
Excluded volume	98889 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1l1l__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1l1l__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1l1l__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1l1l__assembly_4__model_1`	monomeric （1）	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 (2)

Entity 1 Entity 1 polymer

Description description	RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE
Molecular weight formula_weight	82071.0 kDa
EC 编号 ec_number	1.17.4.2
Mutation mutation	C731/736S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	25227

MSEEISLSAEFIDRVKASVKPHWGKLGWVTYKRTYARWLPEKGRSENWDETVKRVVEGNINLDPRLQDSPSLELKQSLTEEAERLYKLIYGLGATPSGRNLWISGTDYQRRTGDSLNNCWFVAIRPQKYGDSKIVPSYLGKQEKAVSMPFSFLFDELMKGGGVGFSVARSNISQIPRVDFAIDLQLVVDETSESYDASVKVGAVGKNELVQDADSIYYRLPDTREGWVLANALLIDLHFAQTNPDRKQKLILDLSDIRPYGAEIHGFGGTASGPMPLISMLLDVNEVLNNKAGGRLTAVDAADICNLIGKAVVAGNVRRSAELALGSNDDQDFISMKQDQEKLMHHRWASNNSVAVDSAFSGYQPIAAGIRENGEPGIVNLDLSKNYGRIVDGYQAGIDGDVEGTNPCGEISLANGEPCNLFEVFPLIAEEQGWDLQEVFALAARYAKRVTFSPYDWEISREIIQKNRRIGISMSGIQDWLLTRLGNRVVTGFKDDFDPETHEAIKVPVYDKRAIKMVDQLYKAVVKADQDYSKTLGCNESIKHTTVKPSGTVAKLAGASEGMHFHYGAYLIQRIRFQDSDPLLPALKACGYRTEADIYTENTTCVEFPIKAVGADNPNFASAGTVSIAEQFATQAFLQTYWSDNAVSCTITFQDSEGDQVESLLRQYRFITKSTSLLPYFGGSLQQAPKEPIDKETYEKRSQEITGNVEEVFSQLNSDVKDLELVDQTDCEGGACPIK

Source Source

Source organism organism	Lactobacillus leichmannii
NCBI taxonomy ID ncbi_taxonomy_id	28039
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2875

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1l1la_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.4 — B12-dependent (class II) ribonucleotide reductase

Domain ID domain_id	d1l1lb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.4 — B12-dependent (class II) ribonucleotide reductase

Domain ID domain_id	d1l1lc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.4 — B12-dependent (class II) ribonucleotide reductase

Domain ID domain_id	d1l1ld_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.4 — B12-dependent (class II) ribonucleotide reductase

CATH v4.4 (12 domains)

Domain ID domain_id	1l1lA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1l1lA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1620 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2
Homologous superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2

Domain ID domain_id	1l1lA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1390 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3
Homologous superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3

Domain ID domain_id	1l1lB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1l1lB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1620 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2
Homologous superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2

Domain ID domain_id	1l1lB03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1390 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3
Homologous superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3

Domain ID domain_id	1l1lC01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1l1lC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1620 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2
Homologous superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2

Domain ID domain_id	1l1lC03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1390 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3
Homologous superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3

Domain ID domain_id	1l1lD01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1l1lD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1620 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2
Homologous superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2

Domain ID domain_id	1l1lD03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1390 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3
Homologous superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3

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Unit-cell length a length_a	120.500 Å
Unit-cell length b length_b	114.700 Å
Unit-cell length c length_c	121.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2230
R_free r_free	0.2660

CRYSTAL STRUCTURE OF B-12 DEPENDENT (CLASS II) RIBONUCLEOTIDE REDUCTASE

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

RIBONUCLEOSIDE TRIPHOSPHATE 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

1l1l__assembly_3__model_1

1l1l__assembly_3__model_1 | I(q)

1l1l__assembly_3__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF B-12 DEPENDENT (CLASS II) RIBONUCLEOTIDE REDUCTASE

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

RIBONUCLEOSIDE TRIPHOSPHATE 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

1l1l__assembly_3__model_1

1l1l__assembly_3__model_1 | I(q)

1l1l__assembly_3__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

7. Citations (1)