SAXSdb — 2odr

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

phosphoseryl-tRNA synthetase

Methanococcus maripaludis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6LZE1_METMP
Isoform	—
PDB entities	1, 2, 3, 4
Chains and sequence ranges	Author chain A； PDBConstruct 20–556； UniProt 1–537 Author chain B； PDBConstruct 20–556； UniProt 1–537 Author chain C； PDBConstruct 20–556； UniProt 1–537 Author chain D； PDBConstruct 20–556； UniProt 1–537

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	2odr
Deposition date deposition_date	2006-12-26
Structure title title	Methanococcus Maripaludis Phosphoseryl-tRNA synthetase
Keywords keywords	phosphoserine tRNA synthetase class II, Ligase; LIGASE
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.

2odr__assembly_1__model_1

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

Download this curve (.dat)

2odr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2odr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.57 Å
Rg (electron density)	39.32 Å
Total Rg	39.55 Å
Atom count	13538
Residues	1858
Excluded volume	239770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2odr__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 (4)

Entity 1 Entity 1 polymer

Description description	phosphoseryl-tRNA synthetase
Molecular weight formula_weight	72593.0 kDa
EC 编号 ec_number	6.1.1.-
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	13538

MGSHHHHHHSSGLVPRGSHMFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIKPVFGKTHPVNDTIENLRQAYLRMGFEEYINPVIVDERDIYKQFGPEAMAVLDRCFYLAGLPRPDVGLSDEKISQIEKLGIKVSEHKESLQKILHGYKKGTLDGDDLVLEISNALEISSEMGLKILEDVFPEFKDLTAVSSKLTLRSHMTSGWFLTVSDLMNKKPLPFKLFSIDRCFRREQKEDKSHLMTYHSASCAIAGEGVDINDGKAIAEGLLSQFGFTNFKFIPDEKKSKYYTPETQTEVYAYHPKLKEWLEVATFGVYSPVALSKYGIDVPVMNLGLGVERLAMISGNFADVREMVYPQFYEHKLNDRNVASMVKLDKVPVMDEIYDLTKELIESCVKNKDLKSPCELAIEKTFSFGKTKKNVKINIFEKEEGKNLLGPSILNEIYVYDGNVIGIPESFDGVKEEFKDFLEKGKSEGVATGIRYIDALCFKITSKLEEAFVSNTTEFKVKVPIVRSLSDINLKIDDIALKQIMSKNKVIDVRGPVFLNVEVKIEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Source Source

Source organism organism	Methanococcus maripaludis
NCBI taxonomy ID ncbi_taxonomy_id	267377
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	phosphoseryl-tRNA synthetase
Molecular weight formula_weight	71146.2 kDa
EC 编号 ec_number	6.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSHHHHHHSSGLVPRGSHMFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIKPVFGKTHPVNDTIENLRQAYLRMGFEEYINPVIVDERDIYKQFGPEAMAVLDRCFYLAGLPRPDVGLSDEKISQIEKLGIKVSEHKESLQKILHGYKKGTLDGDDLVLEISNALEISSEMGLKILEDVFPEFKDLTAVSSKLTLRSHMTSGWFLTVSDLMNKKPLPFKLFSIDRCFRREQKEDKSHLMTYHSASCAIAGEGVDINDGKAIAEGLLSQFGFTNFKFIPDEKKSKYYTPETQTEVYAYHPKLKEWLEVATFGVYSPVALSKYGIDVPVMNLGLGVERLAMISGNFADVREMVYPQFYEHKLNDRNVASMVKLDKVPVMDEIYDLTKELIESCVKNKDLKSPCELAIEKTFSFGKTKKNVKINIFEKEEGKNLLGPSILNEIYVYDGNVIGIPESFDGVKEEFKDFLEKGKSEGVATGIRYIDALCFKITSKLEEAFVSNTTEFKVKVPIVRSLSDINLKIDDIALKQIMSKNKVIDVRGPVFLNVEVKIEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Source Source

Source organism organism	Methanococcus maripaludis
NCBI taxonomy ID ncbi_taxonomy_id	267377
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	phosphoseryl-tRNA synthetase
Molecular weight formula_weight	75656.6 kDa
EC 编号 ec_number	6.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGSHHHHHHSSGLVPRGSHMFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIKPVFGKTHPVNDTIENLRQAYLRMGFEEYINPVIVDERDIYKQFGPEAMAVLDRCFYLAGLPRPDVGLSDEKISQIEKLGIKVSEHKESLQKILHGYKKGTLDGDDLVLEISNALEISSEMGLKILEDVFPEFKDLTAVSSKLTLRSHMTSGWFLTVSDLMNKKPLPFKLFSIDRCFRREQKEDKSHLMTYHSASCAIAGEGVDINDGKAIAEGLLSQFGFTNFKFIPDEKKSKYYTPETQTEVYAYHPKLKEWLEVATFGVYSPVALSKYGIDVPVMNLGLGVERLAMISGNFADVREMVYPQFYEHKLNDRNVASMVKLDKVPVMDEIYDLTKELIESCVKNKDLKSPCELAIEKTFSFGKTKKNVKINIFEKEEGKNLLGPSILNEIYVYDGNVIGIPESFDGVKEEFKDFLEKGKSEGVATGIRYIDALCFKITSKLEEAFVSNTTEFKVKVPIVRSLSDINLKIDDIALKQIMSKNKVIDVRGPVFLNVEVKIEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Source Source

Source organism organism	Methanococcus maripaludis
NCBI taxonomy ID ncbi_taxonomy_id	267377
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	phosphoseryl-tRNA synthetase
Molecular weight formula_weight	74339.0 kDa
EC 编号 ec_number	6.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MGSHHHHHHSSGLVPRGSHMFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIKPVFGKTHPVNDTIENLRQAYLRMGFEEYINPVIVDERDIYKQFGPEAMAVLDRCFYLAGLPRPDVGLSDEKISQIEKLGIKVSEHKESLQKILHGYKKGTLDGDDLVLEISNALEISSEMGLKILEDVFPEFKDLTAVSSKLTLRSHMTSGWFLTVSDLMNKKPLPFKLFSIDRCFRREQKEDKSHLMTYHSASCAIAGEGVDINDGKAIAEGLLSQFGFTNFKFIPDEKKSKYYTPETQTEVYAYHPKLKEWLEVATFGVYSPVALSKYGIDVPVMNLGLGVERLAMISGNFADVREMVYPQFYEHKLNDRNVASMVKLDKVPVMDEIYDLTKELIESCVKNKDLKSPCELAIEKTFSFGKTKKNVKINIFEKEEGKNLLGPSILNEIYVYDGNVIGIPESFDGVKEEFKDFLEKGKSEGVATGIRYIDALCFKITSKLEEAFVSNTTEFKVKVPIVRSLSDINLKIDDIALKQIMSKNKVIDVRGPVFLNVEVKIEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Source Source

Source organism organism	Methanococcus maripaludis
NCBI taxonomy ID ncbi_taxonomy_id	267377
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2odrC01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	250 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2odrC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	2odrD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	2odrD03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3340 —

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Unit-cell length a length_a	119.172 Å
Unit-cell length b length_b	133.943 Å
Unit-cell length c length_c	208.382 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.228 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2920
R_work r_work	0.2920
R_free r_free	0.3060

Methanococcus Maripaludis Phosphoseryl-tRNA synthetase

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

phosphoseryl-tRNA synthetase

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

2odr__assembly_1__model_1

2odr__assembly_1__model_1 | I(q)

2odr__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Methanococcus Maripaludis Phosphoseryl-tRNA synthetase

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

phosphoseryl-tRNA synthetase

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

2odr__assembly_1__model_1

2odr__assembly_1__model_1 | I(q)

2odr__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)