SAXSdb — 1j31

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

Hypothetical protein PH0642

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	ACETATE ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ACETATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O58376_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–262； UniProt 1–262 Author chain B； PDBConstruct 1–262； UniProt 1–262 Author chain C； PDBConstruct 1–262； UniProt 1–262 Author chain D； PDBConstruct 1–262； UniProt 1–262

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	1j31
Deposition date deposition_date	2003-01-16
Structure title title	Crystal Structure of Hypothetical Protein PH0642 from Pyrococcus horikoshii
Keywords keywords	alpha-beta-beta-alpha sandwich, STRUCTURAL GENOMICS, 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.

1j31__assembly_1__model_1

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

Download this curve (.dat)

1j31__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1j31__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.79 Å
Rg (electron density)	24.93 Å
Total Rg	25.72 Å
Atom count	4214
Residues	510
Excluded volume	76070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1j31__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1j31__assembly_2__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 PH0642
Molecular weight formula_weight	30172.7 kDa
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	9070

MVKVGYIQMEPKILELDKNYSKAEKLIKEASKEGAKLVVLPELFDTGYNFESREEVFDVAQQIPEGETTTFLMELARELGLYIVAGTAEKSGNYLYNSAVVVGPRGYIGKYRKIHLFYREKVFFEPGDLGFKVFDIGFAKVGVMICFDWFFPESARTLALKGAEIIAHPANLVMPYAPRAMPIRALENRVYTITADRVGEERGLKFIGKSLIASPKAEVLSIASETEEEIGVVEIDLNLARNKRLNDMNDIFKDRREEYYFR

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	ACETATE ION
Molecular weight formula_weight	59.0 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	642

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1j31a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.160 — Carbon-nitrogen hydrolase
Superfamily Superfamily superfamily	d.160.1 — Carbon-nitrogen hydrolase
Family Family family	d.160.1.2 — Carbamilase

Domain ID domain_id	d1j31b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.160 — Carbon-nitrogen hydrolase
Superfamily Superfamily superfamily	d.160.1 — Carbon-nitrogen hydrolase
Family Family family	d.160.1.2 — Carbamilase

Domain ID domain_id	d1j31c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.160 — Carbon-nitrogen hydrolase
Superfamily Superfamily superfamily	d.160.1 — Carbon-nitrogen hydrolase
Family Family family	d.160.1.2 — Carbamilase

Domain ID domain_id	d1j31d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.160 — Carbon-nitrogen hydrolase
Superfamily Superfamily superfamily	d.160.1 — Carbon-nitrogen hydrolase
Family Family family	d.160.1.2 — Carbamilase

CATH v4.4 (4 domains)

Domain ID domain_id	1j31A00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
Homologous superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

Domain ID domain_id	1j31B00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
Homologous superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

Domain ID domain_id	1j31C00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
Homologous superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

Domain ID domain_id	1j31D00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
Homologous superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

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Unit-cell length a length_a	75.037 Å
Unit-cell length b length_b	89.021 Å
Unit-cell length c length_c	77.871 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.15 °
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	1.600 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1660
R_work r_work	0.1660
R_free r_free	0.1940

Crystal Structure of Hypothetical Protein PH0642 from Pyrococcus horikoshii

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

Hypothetical protein PH0642

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

1j31__assembly_1__model_1

1j31__assembly_1__model_1 | I(q)

1j31__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Hypothetical Protein PH0642 from Pyrococcus horikoshii

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

Hypothetical protein PH0642

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

1j31__assembly_1__model_1

1j31__assembly_1__model_1 | I(q)

1j31__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)