2eky

Crystal Structure of hypothetical protein MJ1052 from Methanocaldococcus jannaschii (Form 1)

Method: X-RAY DIFFRACTION

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

UPF0045 protein MJ1052

Methanocaldococcus jannaschii

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 4	water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1052_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–100； UniProt 1–100 Author chain B； PDBConstruct 1–100； UniProt 1–100 Author chain C； PDBConstruct 1–100； UniProt 1–100 Author chain D； PDBConstruct 1–100； UniProt 1–100 Author chain E； PDBConstruct 1–100； UniProt 1–100 Author chain F； PDBConstruct 1–100； UniProt 1–100 Author chain G； PDBConstruct 1–100； UniProt 1–100 Author chain H； PDBConstruct 1–100； UniProt 1–100

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	2eky
Deposition date deposition_date	2007-03-26
Structure title title	Crystal Structure of hypothetical protein MJ1052 from Methanocaldococcus jannaschii (Form 1)
Keywords keywords	;STRUCTURAL GENOMICS, UNKNOWN FUNCTION, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; 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.

2eky__assembly_1__model_1

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

Download this curve (.dat)

2eky__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2eky__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.93 Å
Rg (electron density)	19.65 Å
Total Rg	20.71 Å
Atom count	3097
Residues	394
Excluded volume	56433 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2eky__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2eky__assembly_2__model_1`	tetrameric （4）	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) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2ekya_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.48 — MTH1187/YkoF-like
Family Family family	d.58.48.0 — automated matches

Domain ID domain_id	d2ekyb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.48 — MTH1187/YkoF-like
Family Family family	d.58.48.0 — automated matches

Domain ID domain_id	d2ekyc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.48 — MTH1187/YkoF-like
Family Family family	d.58.48.0 — automated matches

Domain ID domain_id	d2ekyd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.48 — MTH1187/YkoF-like
Family Family family	d.58.48.0 — automated matches

Domain ID domain_id	d2ekye_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.48 — MTH1187/YkoF-like
Family Family family	d.58.48.0 — automated matches

Domain ID domain_id	d2ekyf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.48 — MTH1187/YkoF-like
Family Family family	d.58.48.0 — automated matches

Domain ID domain_id	d2ekyg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.48 — MTH1187/YkoF-like
Family Family family	d.58.48.0 — automated matches

Domain ID domain_id	d2ekyh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.48 — MTH1187/YkoF-like
Family Family family	d.58.48.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	2ekyA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	930 —

Domain ID domain_id	2ekyB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	930 —

Domain ID domain_id	2ekyC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	930 —

Domain ID domain_id	2ekyD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	930 —

Domain ID domain_id	2ekyE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	930 —

Domain ID domain_id	2ekyF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	930 —

Domain ID domain_id	2ekyG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	930 —

Domain ID domain_id	2ekyH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	930 —

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Unit-cell length a length_a	73.437 Å
Unit-cell length b length_b	61.394 Å
Unit-cell length c length_c	87.811 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1920
R_work r_work	0.1920
R_free r_free	0.2320

Description description	UPF0045 protein MJ1052
Molecular weight formula_weight	11243.2 kDa
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	6861

Crystal Structure of hypothetical protein MJ1052 from Methanocaldococcus jannaschii (Form 1)

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

UPF0045 protein MJ1052

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

2eky__assembly_1__model_1

2eky__assembly_1__model_1 | I(q)

2eky__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	243232
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	731

Crystal Structure of hypothetical protein MJ1052 from Methanocaldococcus jannaschii (Form 1)

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

UPF0045 protein MJ1052

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

2eky__assembly_1__model_1

2eky__assembly_1__model_1 | I(q)

2eky__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)