SAXSdb — 3ghd

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

a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain

Pyrococcus furiosus

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8TZN4_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–70； UniProt 14–83 Author chain B； PDBConstruct 1–70； UniProt 14–83

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	3ghd
Deposition date deposition_date	2009-03-03
Structure title title	Crystal structure of a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain
Keywords keywords	;PF1953, APC40009, cystathionine beta-synthase domain protein, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, NUCLEOTIDE BINDING PROTEIN, METAL BINDIN, Metal binding protein ;; Nucleotide 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.

3ghd__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3ghd__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ghd__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	17.08 Å
Rg (electron density)	16.34 Å
Total Rg	17.54 Å
Atom count	1027
Residues	136
Excluded volume	18789 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ghd__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ghd__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3ghd__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 (2)

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3ghdA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1280 — CBS domain Like
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3ghdB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1280 — CBS domain Like
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	54.153 Å
Unit-cell length b length_b	73.162 Å
Unit-cell length c length_c	35.264 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	31.770 Å
R factor r_factor	0.1946
R_work r_work	0.1923
R_free r_free	0.2411

Description description	a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain
Molecular weight formula_weight	7746.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1139

Crystal structure of a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain

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

a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain

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

3ghd__assembly_2__model_1

3ghd__assembly_2__model_1 | I(q)

3ghd__assembly_2__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	112

Crystal structure of a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain

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

a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain

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

3ghd__assembly_2__model_1

3ghd__assembly_2__model_1 | I(q)

3ghd__assembly_2__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)