SAXSdb — 1z2z

▼

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

Probable tRNA pseudouridine synthase D

Methanosarcina mazei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRUD_METMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–438； UniProt 1–438 Author chain B； PDBConstruct 1–438； UniProt 1–438

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1z2z
Deposition date deposition_date	2005-03-10
Structure title title	Crystal Structure of the Putative tRNA pseudouridine synthase D (TruD) from Methanosarcina mazei, Northeast Structural Genomics Target MaR1
Keywords keywords	alpha-beta protein., Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, LYASE; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1z2z__assembly_1__model_1

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

Download this curve (.dat)

1z2z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1z2z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.09 Å
Rg (electron density)	24.00 Å
Total Rg	24.81 Å
Atom count	3478
Residues	428
Excluded volume	62294 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1z2z__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1z2z__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Probable tRNA pseudouridine synthase D
Molecular weight formula_weight	51057.7 kDa
EC 编号 ec_number	4.2.1.70
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	7176

MEVPEIEKQIGINLYSTDTTGLGGQLRQEIEDFIVKEITNREEGEEGKYLIVELTKRDWDTHHLTRTLSRILQVSQKRISVAGTKDKRALTTQKISIFDTDASEIEKIHLKDIELKVLGRSRKSVELGDLWGNDFRITVRNIENSPEETEALLKKTTDEILAQGGVPNFFGIQRFGSVRPVTHLVGKAIVEGNFEKAALLYIAEPFPEEPEETKNARQFVKDTLDFKEGLKTYPLRLGHERAMMNHLIANPEDYSGSFRVLPQNLYRMFVHGYQSYIYNIILCRRIEAGIPLNRAVEGDIVCFRNEVGLPDSSKTEKVTSETVNAMNRLLKLGRAFITAPLPGYNTEFASGIPGEIENGVLKELGVSLEGFNIEKFPEMSSKGTRREVLLEVKPKFEAGEDELNPGKSKAVLEFMLPKGSYATTVLREYMKVNPLQMSLEHHHHHH

Source Source

Source organism organism	Methanosarcina mazei
NCBI taxonomy ID ncbi_taxonomy_id	2209
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	220

▼

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	1z2zA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2350 — Pseudouridine synthase
Homologous superfamily homologous superfamily	20 — TruD, catalytic domain

Domain ID domain_id	1z2zA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3160 —

Domain ID domain_id	1z2zA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1510 — Hypothetical Protein Yqey; Chain: A; domain1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1z2zB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2350 — Pseudouridine synthase
Homologous superfamily homologous superfamily	20 — TruD, catalytic domain

Domain ID domain_id	1z2zB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3160 —

Domain ID domain_id	1z2zB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1510 — Hypothetical Protein Yqey; Chain: A; domain1
Homologous superfamily homologous superfamily	30 —

▶

Unit-cell length a length_a	62.562 Å
Unit-cell length b length_b	132.531 Å
Unit-cell length c length_c	66.779 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	29.030 Å
R factor r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.2960

Crystal Structure of the Putative tRNA pseudouridine synthase D (TruD) from Methanosarcina mazei, Northeast Structural Genomics Target MaR1

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

Probable tRNA pseudouridine synthase D

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

1z2z__assembly_1__model_1

1z2z__assembly_1__model_1 | I(q)

1z2z__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

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of the Putative tRNA pseudouridine synthase D (TruD) from Methanosarcina mazei, Northeast Structural Genomics Target MaR1

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

Probable tRNA pseudouridine synthase D

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

1z2z__assembly_1__model_1

1z2z__assembly_1__model_1 | I(q)

1z2z__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

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)