SAXSdb — 1xzp

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

Probable tRNA modification GTPase trmE

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 5 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 10 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRME_THEMA
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 33–482； UniProt 1–450 Author chain B； PDBConstruct 33–150； UniProt 1–118

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	1xzp
Deposition date deposition_date	2004-11-12
Structure title title	Structure of the GTP-binding protein TrmE from Thermotoga maritima
Keywords keywords	GTP-binding, THF-binding, tRNA-modification, HYDROLASE; 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.

1xzp__assembly_1__model_1

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

Download this curve (.dat)

1xzp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xzp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.71 Å
Rg (electron density)	28.98 Å
Total Rg	29.59 Å
Atom count	4571
Residues	587
Excluded volume	81883 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xzp__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1xzp__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 (4)

Entity 1 Entity 1 polymer

Description description	Probable tRNA modification GTPase trmE
Molecular weight formula_weight	54189.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4708

MGSSHHHHHHSSGLVPRGSHWGSPNSSSVDKLMDTIVAVATPPGKGAIAILRLSGPDSWKIVQKHLRTRSKIVPRKAIHGWIHENGEDVDEVVVVFYKSPKSYTGEDMVEVMCHGGPLVVKKLLDLFLKSGARMAEPGEFTKRAFLNGKMDLTSAEAVRDLIEAKSETSLKLSLRNLKGGLRDFVDSLRRELIEVLAEIRVELDYPDEIETNTGEVVTRLERIKEKLTEELKKADAGILLNRGLRMVIVGKPNVGKSTLLNRLLNEDRAIVTDIPGTTRDVISEEIVIRGILFRIVDTAGVRSETNDLVERLGIERTLQEIEKADIVLFVLDASSPLDEEDRKILERIKNKRYLVVINKVDVVEKINEEEIKNKLGTDRHMVKISALKGEGLEKLEESIYRETQEIFERGSDSLITNLRQKQLLENVKGHLEDAIKSLKEGMPVDMASIDLERALNLLDEVTGRSFREDLLDTIFSNFCVGK

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Probable tRNA modification GTPase trmE
Molecular weight formula_weight	16495.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSSHHHHHHSSGLVPRGSHWGSPNSSSVDKLMDTIVAVATPPGKGAIAILRLSGPDSWKIVQKHLRTRSKIVPRKAIHGWIHENGEDVDEVVVVFYKSPKSYTGEDMVEVMCHGGPLVVKKLLDLFLKSGARMAEPGEFTKRAFLNGKM

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	137

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1xzpa1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.25 — TrmE connector domain
Family Family family	a.24.25.1 — TrmE connector domain

Domain ID domain_id	d1xzpa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d1xzpa3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.250 — Folate-binding domain
Superfamily Superfamily superfamily	d.250.1 — Folate-binding domain
Family Family family	d.250.1.2 — TrmE formyl-THF-binding domain

Domain ID domain_id	d1xzpa4
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	d1xzpb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.250 — Folate-binding domain
Superfamily Superfamily superfamily	d.250.1 — Folate-binding domain
Family Family family	d.250.1.2 — TrmE formyl-THF-binding domain

Domain ID domain_id	d1xzpb2
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	1xzpA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	120 — Probable tRNA modification gtpase trme; domain 1

Domain ID domain_id	1xzpA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	430 — tRNA modification GTPase MnmE domain 2

Domain ID domain_id	1xzpA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1xzpB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	120 — Probable tRNA modification gtpase trme; domain 1

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Unit-cell length a length_a	128.855 Å
Unit-cell length b length_b	128.855 Å
Unit-cell length c length_c	107.161 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 62
Space-group number int_tables_number	171
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	19.700 Å
R factor r_factor	0.2270
R_work r_work	0.2260
R_free r_free	0.2520

Structure of the GTP-binding protein TrmE from Thermotoga maritima

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

Probable tRNA modification GTPase trmE

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

1xzp__assembly_1__model_1

1xzp__assembly_1__model_1 | I(q)

1xzp__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the GTP-binding protein TrmE from Thermotoga maritima

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

Probable tRNA modification GTPase trmE

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

1xzp__assembly_1__model_1

1xzp__assembly_1__model_1 | I(q)

1xzp__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)