2zv3

Crystal structure of project MJ0051 from Methanocaldococcus jannaschii DSM 2661

Method: X-RAY DIFFRACTION

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

Peptidyl-tRNA hydrolase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PTH_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–115； UniProt 1–115 Author chain B； PDBConstruct 1–115； UniProt 1–115 Author chain C； PDBConstruct 1–115； UniProt 1–115 Author chain D； PDBConstruct 1–115； UniProt 1–115 Author chain E； PDBConstruct 1–115； UniProt 1–115 Author chain F； PDBConstruct 1–115； UniProt 1–115 Author chain G； PDBConstruct 1–115； UniProt 1–115 Author chain H； PDBConstruct 1–115； UniProt 1–115 Author chain I； PDBConstruct 1–115； UniProt 1–115

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	2zv3
Deposition date deposition_date	2008-10-31
Structure title title	Crystal structure of project MJ0051 from Methanocaldococcus jannaschii DSM 2661
Keywords keywords	;Cytoplasm, Hydrolase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; HYDROLASE
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.

2zv3__assembly_1__model_1

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

Download this curve (.dat)

2zv3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zv3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.16 Å
Rg (electron density)	16.93 Å
Total Rg	17.93 Å
Atom count	1720
Residues	223
Excluded volume	31105 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zv3__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zv3__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2zv3__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2zv3__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2zv3__assembly_5__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 (2)

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2zv3a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.131 — Peptidyl-tRNA hydrolase II
Superfamily Superfamily superfamily	c.131.1 — Peptidyl-tRNA hydrolase II
Family Family family	c.131.1.0 — automated matches

Domain ID domain_id	d2zv3b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.131 — Peptidyl-tRNA hydrolase II
Superfamily Superfamily superfamily	c.131.1 — Peptidyl-tRNA hydrolase II
Family Family family	c.131.1.0 — automated matches

Domain ID domain_id	d2zv3c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.131 — Peptidyl-tRNA hydrolase II
Superfamily Superfamily superfamily	c.131.1 — Peptidyl-tRNA hydrolase II
Family Family family	c.131.1.0 — automated matches

Domain ID domain_id	d2zv3d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.131 — Peptidyl-tRNA hydrolase II
Superfamily Superfamily superfamily	c.131.1 — Peptidyl-tRNA hydrolase II
Family Family family	c.131.1.0 — automated matches

Domain ID domain_id	d2zv3e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.131 — Peptidyl-tRNA hydrolase II
Superfamily Superfamily superfamily	c.131.1 — Peptidyl-tRNA hydrolase II
Family Family family	c.131.1.0 — automated matches

Domain ID domain_id	d2zv3f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.131 — Peptidyl-tRNA hydrolase II
Superfamily Superfamily superfamily	c.131.1 — Peptidyl-tRNA hydrolase II
Family Family family	c.131.1.0 — automated matches

Domain ID domain_id	d2zv3g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.131 — Peptidyl-tRNA hydrolase II
Superfamily Superfamily superfamily	c.131.1 — Peptidyl-tRNA hydrolase II
Family Family family	c.131.1.0 — automated matches

Domain ID domain_id	d2zv3h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.131 — Peptidyl-tRNA hydrolase II
Superfamily Superfamily superfamily	c.131.1 — Peptidyl-tRNA hydrolase II
Family Family family	c.131.1.0 — automated matches

Domain ID domain_id	d2zv3i_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.131 — Peptidyl-tRNA hydrolase II
Superfamily Superfamily superfamily	c.131.1 — Peptidyl-tRNA hydrolase II
Family Family family	c.131.1.0 — automated matches

CATH v4.4 (9 domains)

Domain ID domain_id	2zv3A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1490 — Bit1
Homologous superfamily homologous superfamily	10 — Bit1

Domain ID domain_id	2zv3B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1490 — Bit1
Homologous superfamily homologous superfamily	10 — Bit1

Domain ID domain_id	2zv3C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1490 — Bit1
Homologous superfamily homologous superfamily	10 — Bit1

Domain ID domain_id	2zv3D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1490 — Bit1
Homologous superfamily homologous superfamily	10 — Bit1

Domain ID domain_id	2zv3E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1490 — Bit1
Homologous superfamily homologous superfamily	10 — Bit1

Domain ID domain_id	2zv3F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1490 — Bit1
Homologous superfamily homologous superfamily	10 — Bit1

Domain ID domain_id	2zv3G00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1490 — Bit1
Homologous superfamily homologous superfamily	10 — Bit1

Domain ID domain_id	2zv3H00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1490 — Bit1
Homologous superfamily homologous superfamily	10 — Bit1

Domain ID domain_id	2zv3I00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1490 — Bit1
Homologous superfamily homologous superfamily	10 — Bit1

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Unit-cell length a length_a	149.850 Å
Unit-cell length b length_b	70.790 Å
Unit-cell length c length_c	96.010 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	121.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	36

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	40.920 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2630

Description description	Peptidyl-tRNA hydrolase
Molecular weight formula_weight	12692.9 kDa
EC 编号 ec_number	3.1.1.29
Source method src_method	nat
Copy count entity_count	9

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I
Atom count atom_count	8466

Crystal structure of project MJ0051 from Methanocaldococcus jannaschii DSM 2661

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

Peptidyl-tRNA hydrolase

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

2zv3__assembly_1__model_1

2zv3__assembly_1__model_1 | I(q)

2zv3__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	731

Crystal structure of project MJ0051 from Methanocaldococcus jannaschii DSM 2661

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

Peptidyl-tRNA hydrolase

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

2zv3__assembly_1__model_1

2zv3__assembly_1__model_1 | I(q)

2zv3__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)