SAXSdb — 3bbd

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

Ribosome biogenesis protein NEP1-like

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	S-ADENOSYL-L-HOMOCYSTEINE × 2 GLYCEROL × 7 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NEP1_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–205； UniProt 1–205 Author chain B； PDBConstruct 1–205； UniProt 1–205

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	3bbd
Deposition date deposition_date	2007-11-09
Structure title title	M. jannaschii Nep1 complexed with S-adenosyl-homocysteine
Keywords keywords	methyltransferase, ribosome biogenesis, S-adenosyl-methionine, S-adenosyl-homocysteine, rRNA processing, TRANSFERASE; TRANSFERASE
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.

3bbd__assembly_1__model_1

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

Download this curve (.dat)

3bbd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bbd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.98 Å
Rg (electron density)	21.85 Å
Total Rg	22.85 Å
Atom count	3466
Residues	396
Excluded volume	63391 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bbd__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 (4)

Entity 1 Entity 1 polymer

Description description	Ribosome biogenesis protein NEP1-like
Molecular weight formula_weight	24453.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3750

MTYNIILAKSALELIPEEIKNKIRKSRVYKYDILDSNYHYKAMEKLKDKEMRGRPDIIHISLLNILDSPINHEKKLNIYIHTYDDKVLKINPETRLPRNYFRFLGVMEKVLKGERNHLIKMEEKTLEDLLNEINAKKIAIMTKTGKLTHPKLLKEYDTFIIGGFPYGKLKINKEKVFGDIKEISIYNKGLMAWTVCGIICYSLSF

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	265

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3bbda1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.6 — EMG1/NEP1-like

Domain ID domain_id	d3bbdb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.6 — EMG1/NEP1-like

CATH v4.4 (2 domains)

Domain ID domain_id	3bbdA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

Domain ID domain_id	3bbdB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

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Unit-cell length a length_a	84.894 Å
Unit-cell length b length_b	91.121 Å
Unit-cell length c length_c	93.713 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	46.856 Å
R factor r_factor	0.1819
R_work r_work	0.1798
R_free r_free	0.2210

M. jannaschii Nep1 complexed with S-adenosyl-homocysteine

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

Ribosome biogenesis protein NEP1-like

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

3bbd__assembly_1__model_1

3bbd__assembly_1__model_1 | I(q)

3bbd__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

M. jannaschii Nep1 complexed with S-adenosyl-homocysteine

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

Ribosome biogenesis protein NEP1-like

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

3bbd__assembly_1__model_1

3bbd__assembly_1__model_1 | I(q)

3bbd__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)