SAXSdb — 2cxi

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

Phenylalanyl-tRNA synthetase beta chain

Pyrococcus horikoshii

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYFB_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–348； UniProt 1–348 Author chain B； PDBConstruct 1–348； UniProt 1–348 Author chain C； PDBConstruct 1–348； UniProt 1–348

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	2cxi
Deposition date deposition_date	2005-06-29
Structure title title	Crystal Structure Of An N-terminal Fragment Of The Phenylalanyl-tRNA Synthetase Beta-Subunit From Pyrococcus Horikoshii
Keywords keywords	;Aminoacyl-tRNA synthetase, Ligase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; 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.

2cxi__assembly_1__model_1

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

Download this curve (.dat)

2cxi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2cxi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.45 Å
Rg (electron density)	35.93 Å
Total Rg	36.26 Å
Atom count	8526
Residues	1017
Excluded volume	153860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2cxi__assembly_1__model_1`	trimeric （3）	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) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	2cxiA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2cxiA02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3
Homologous superfamily homologous superfamily	10 — Phenylalanyl-trna Synthetase, Chain B, domain 3

Domain ID domain_id	2cxiA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2cxiB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2cxiB02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3
Homologous superfamily homologous superfamily	10 — Phenylalanyl-trna Synthetase, Chain B, domain 3

Domain ID domain_id	2cxiB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2cxiC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2cxiC02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3
Homologous superfamily homologous superfamily	10 — Phenylalanyl-trna Synthetase, Chain B, domain 3

Domain ID domain_id	2cxiC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	142.779 Å
Unit-cell length b length_b	81.973 Å
Unit-cell length c length_c	139.096 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.79 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	41.520 Å
R factor r_factor	0.1898
R_work r_work	0.1877
R_free r_free	0.2307

Description description	Phenylalanyl-tRNA synthetase beta chain
Molecular weight formula_weight	40915.6 kDa
EC 编号 ec_number	6.1.1.20
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	9228

Crystal Structure Of An N-terminal Fragment Of The Phenylalanyl-tRNA Synthetase Beta-Subunit From Pyrococcus Horikoshii

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

Phenylalanyl-tRNA synthetase beta chain

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

2cxi__assembly_1__model_1

2cxi__assembly_1__model_1 | I(q)

2cxi__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) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	684

Crystal Structure Of An N-terminal Fragment Of The Phenylalanyl-tRNA Synthetase Beta-Subunit From Pyrococcus Horikoshii

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

Phenylalanyl-tRNA synthetase beta chain

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

2cxi__assembly_1__model_1

2cxi__assembly_1__model_1 | I(q)

2cxi__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) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)