2php

Crystal structure of the C-terminal domain of protein MJ0236 (Y236_METJA)

Method: X-RAY DIFFRACTION

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

Uncharacterized protein MJ0236

Methanocaldococcus jannaschii DSM 2661

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	CHLORIDE ION × 9 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y236_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–184； UniProt 240–420 Author chain B； PDBConstruct 4–184； UniProt 240–420 Author chain D； PDBConstruct 4–184； UniProt 240–420 Author chain E； PDBConstruct 4–184； UniProt 240–420

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	2php
Deposition date deposition_date	2007-04-11
Structure title title	Crystal structure of the C-terminal domain of protein MJ0236 (Y236_METJA)
Keywords keywords	;Chlorine ion, PSI-2, 10417a, NYSGXRC, Structural Genomics, Protein Structure Initiative, New York SGX Research Center for 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.

2php__assembly_1__model_1

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

Download this curve (.dat)

2php__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2php__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.43 Å
Rg (electron density)	28.49 Å
Total Rg	29.11 Å
Atom count	5779
Residues	718
Excluded volume	105480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2php__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Uncharacterized protein MJ0236
Molecular weight formula_weight	21859.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E
Atom count atom_count	6109

MSLTYINKEKVIKNLSYAIYLLKKMNFTLIPEVGSNIAESLPFPKDFKDVAALTGRIIKNKLGGFYIVGDIEFGASEHIAKIILSASKFNPEIRACMNIKYDGGLIKLLKDKFAVSSFDRKEEPPNVSTMEWGTKIACEKFGGVPDIIYDRGGEGKEPMIRVLGRDAIEVVKKVEVIQKIYNTLEGHHHHHH

Source Source

Source organism organism	Methanocaldococcus jannaschii DSM 2661
NCBI taxonomy ID ncbi_taxonomy_id	243232
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	330

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d2phpa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.74 — AraD/HMP-PK domain-like
Superfamily Superfamily superfamily	c.74.1 — AraD/HMP-PK domain-like
Family Family family	c.74.1.2 — Phosphomethylpyrimidine kinase C-terminal domain-like

Domain ID domain_id	d2phpa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2phpb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.74 — AraD/HMP-PK domain-like
Superfamily Superfamily superfamily	c.74.1 — AraD/HMP-PK domain-like
Family Family family	c.74.1.2 — Phosphomethylpyrimidine kinase C-terminal domain-like

Domain ID domain_id	d2phpb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2phpb4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2phpd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.74 — AraD/HMP-PK domain-like
Superfamily Superfamily superfamily	c.74.1 — AraD/HMP-PK domain-like
Family Family family	c.74.1.2 — Phosphomethylpyrimidine kinase C-terminal domain-like

Domain ID domain_id	d2phpd3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2phpd4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2phpe2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.74 — AraD/HMP-PK domain-like
Superfamily Superfamily superfamily	c.74.1 — AraD/HMP-PK domain-like
Family Family family	c.74.1.2 — Phosphomethylpyrimidine kinase C-terminal domain-like

Domain ID domain_id	d2phpe3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	2phpA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	225 — L-fuculose-1-phosphate Aldolase
Homologous superfamily homologous superfamily	10 — Class II aldolase/adducin N-terminal domain

Domain ID domain_id	2phpB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	225 — L-fuculose-1-phosphate Aldolase
Homologous superfamily homologous superfamily	10 — Class II aldolase/adducin N-terminal domain

Domain ID domain_id	2phpD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	225 — L-fuculose-1-phosphate Aldolase
Homologous superfamily homologous superfamily	10 — Class II aldolase/adducin N-terminal domain

Domain ID domain_id	2phpE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	225 — L-fuculose-1-phosphate Aldolase
Homologous superfamily homologous superfamily	10 — Class II aldolase/adducin N-terminal domain

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Unit-cell length a length_a	147.077 Å
Unit-cell length b length_b	112.141 Å
Unit-cell length c length_c	67.253 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.030 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2162
R_work r_work	0.2162
R_free r_free	0.2380

Crystal structure of the C-terminal domain of protein MJ0236 (Y236_METJA)

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

Uncharacterized protein MJ0236

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

2php__assembly_1__model_1

2php__assembly_1__model_1 | I(q)

2php__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) 14 domains

SCOP 2.08 (10 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the C-terminal domain of protein MJ0236 (Y236_METJA)

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

Uncharacterized protein MJ0236

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

2php__assembly_1__model_1

2php__assembly_1__model_1 | I(q)

2php__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) 14 domains

SCOP 2.08 (10 domains)

CATH v4.4 (4 domains)

7. Citations (1)