SAXSdb — 1vbk

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

hypothetical protein PH1313

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	(4R)-2-METHYLPENTANE-2,4-DIOL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O59053_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–307； UniProt 1–307 Author chain B； PDBConstruct 1–307； UniProt 1–307

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	1vbk
Deposition date deposition_date	2004-02-27
Structure title title	Crystal structure of PH1313 from Pyrococcus horikoshii Ot3
Keywords keywords	;Pyrococcus horikoshii, structural genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, NPPSFA, National Project on Protein Structural and Functional Analyses, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

1vbk__assembly_1__model_1

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

Download this curve (.dat)

1vbk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vbk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.07 Å
Rg (electron density)	33.90 Å
Total Rg	34.21 Å
Atom count	4903
Residues	603
Excluded volume	89323 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	hypothetical protein PH1313
Molecular weight formula_weight	35202.2 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	5540

MNVVIVRYGEIGTKSRQTRSWFEKILMNNIREALVTEEVPYKEIFSRHGRIIVKTNSPKEAANVLVRVFGIVSISPAMEVEASLEKINRTALLMFRKKAKEVGKERPKFRVTARRITKEFPLDSLEIQAKVGEYILNNENCEVDLKNYDIEIGIEIMQGKAYIYTEKIKGWGGLPIGTEGRMIGILHDELSALAIFLMMKRGVEVIPVYIGKDDKNLEKVRSLWNLLKRYSYGSKGFLVVAESFDRVLKLIRDFGVKGVIKGLRPNDLNSEVSEITEDFKMFPVPVYYPLIALPEEYIKSVKERLGL

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(4R)-2-METHYLPENTANE-2,4-DIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	637

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1vbka1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.6 — ThiI-like

Domain ID domain_id	d1vbka2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.308 — THUMP domain
Superfamily Superfamily superfamily	d.308.1 — THUMP domain-like
Family Family family	d.308.1.1 — THUMP domain

Domain ID domain_id	d1vbkb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.6 — ThiI-like

Domain ID domain_id	d1vbkb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.308 — THUMP domain
Superfamily Superfamily superfamily	d.308.1 — THUMP domain-like
Family Family family	d.308.1.1 — THUMP domain

CATH v4.4 (6 domains)

Domain ID domain_id	1vbkA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1510 — THUMP domain-like

Domain ID domain_id	1vbkA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2300 — THUMP fold
Homologous superfamily homologous superfamily	10 — THUMP superfamily

Domain ID domain_id	1vbkA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1vbkB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1510 — THUMP domain-like

Domain ID domain_id	1vbkB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2300 — THUMP fold
Homologous superfamily homologous superfamily	10 — THUMP superfamily

Domain ID domain_id	1vbkB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

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Unit-cell length a length_a	71.743 Å
Unit-cell length b length_b	71.164 Å
Unit-cell length c length_c	141.774 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	1.900 Å
Low-resolution limit resolution_low	39.470 Å
R factor r_factor	0.2030
R_work r_work	0.1990
R_free r_free	0.2220

Crystal structure of PH1313 from Pyrococcus horikoshii Ot3

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

hypothetical protein PH1313

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

1vbk__assembly_1__model_1

1vbk__assembly_1__model_1 | I(q)

1vbk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of PH1313 from Pyrococcus horikoshii Ot3

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

hypothetical protein PH1313

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

1vbk__assembly_1__model_1

1vbk__assembly_1__model_1 | I(q)

1vbk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)