SAXSdb — 3bp1

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

NADPH-dependent 7-cyano-7-deazaguanine reductase

Vibrio cholerae O1 biovar eltor str. N16961

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	PHOSPHATE ION × 6 MAGNESIUM ION × 2 GUANINE × 4 PYROPHOSPHATE 2- × 2 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 3 MAGNESIUM ION × 1 GUANINE × 2 PYROPHOSPHATE 2- × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 3 MAGNESIUM ION × 1 GUANINE × 2 PYROPHOSPHATE 2- × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A6Y463_VIBCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–290； UniProt 1–287 Author chain B； PDBConstruct 4–290； UniProt 1–287 Author chain C； PDBConstruct 4–290； UniProt 1–287 Author chain D； PDBConstruct 4–290； UniProt 1–287

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	3bp1
Deposition date deposition_date	2007-12-18
Structure title title	Crystal structure of putative 7-cyano-7-deazaguanine reductase QueF from Vibrio cholerae O1 biovar eltor
Keywords keywords	;alpha-beta structure, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, 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.

3bp1__assembly_1__model_1

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

Download this curve (.dat)

3bp1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bp1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.01 Å
Rg (electron density)	31.40 Å
Total Rg	31.86 Å
Atom count	8291
Residues	1003
Excluded volume	144850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bp1__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3bp1__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3bp1__assembly_3__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 (6)

Entity 1 Entity 1 polymer

Description description	NADPH-dependent 7-cyano-7-deazaguanine reductase
Molecular weight formula_weight	33315.3 kDa
EC 编号 ec_number	1.7.1.13
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	10479

SNAMNRLKNMSKYSDAKELASLTLGKKTEYANQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTMQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSNCLITNQPDWGSVEIAYHGAKMNREALLRYLVSFREHNEFHEQCVERIFTDIMRYCQPQSLTVYARYTRRGGLDINPFRSSHQSAPNHNQRMARQ

Source Source

Source organism organism	Vibrio cholerae O1 biovar eltor str. N16961
NCBI taxonomy ID ncbi_taxonomy_id	243277
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GUANINE
Molecular weight formula_weight	151.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1177

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3bp1A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	3bp1A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	3bp1B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	3bp1B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	3bp1C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	3bp1C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	3bp1D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	3bp1D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

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Unit-cell length a length_a	71.517 Å
Unit-cell length b length_b	71.578 Å
Unit-cell length c length_c	71.511 Å
Unit-cell angle α angle_alpha	119.25 °
Unit-cell angle β angle_beta	110.18 °
Unit-cell angle γ angle_gamma	99.58 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.530 Å
Low-resolution limit resolution_low	26.160 Å
R factor r_factor	0.1450
R_work r_work	0.1430
R_free r_free	0.1830

Crystal structure of putative 7-cyano-7-deazaguanine reductase QueF from Vibrio cholerae O1 biovar eltor

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

NADPH-dependent 7-cyano-7-deazaguanine 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

3bp1__assembly_1__model_1

3bp1__assembly_1__model_1 | I(q)

3bp1__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of putative 7-cyano-7-deazaguanine reductase QueF from Vibrio cholerae O1 biovar eltor

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

NADPH-dependent 7-cyano-7-deazaguanine 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

3bp1__assembly_1__model_1

3bp1__assembly_1__model_1 | I(q)

3bp1__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)