SAXSdb — 2rhq

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

Phenylalanyl-tRNA synthetase alpha chain

Staphylococcus haemolyticus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Phenylalanyl-tRNA synthetase beta chain × 2 （Q4L5E4） ZINC ION × 2 1-{3-[(4-pyridin-2-ylpiperazin-1-yl)sulfonyl]phenyl}-3-(1,3-thiazol-2-yl)urea × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYFA_STAHJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 27–294； UniProt 84–351

Phenylalanyl-tRNA synthetase beta chain

Staphylococcus haemolyticus

UniProt Q4L5E4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Phenylalanyl-tRNA synthetase alpha chain × 2 （Q4L5E3） ZINC ION × 2 1-{3-[(4-pyridin-2-ylpiperazin-1-yl)sulfonyl]phenyl}-3-(1,3-thiazol-2-yl)urea × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYFB_STAHJ
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–795； UniProt 1–799

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	2rhq
Deposition date deposition_date	2007-10-09
Structure title title	PheRS from Staphylococcus haemolyticus- rational protein engineering and inhibitor studies
Keywords keywords	;heterotetramer, phenylalanine, tRNA, Aminoacyl-tRNA synthetase, ATP-binding, Cytoplasm, Ligase, Magnesium, Metal-binding, Nucleotide-binding, Protein biosynthesis, RNA-binding, tRNA-binding ;; 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.

2rhq__assembly_1__model_1

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

Download this curve (.dat)

2rhq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rhq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.35 Å
Rg (electron density)	49.38 Å
Total Rg	49.47 Å
Atom count	16700
Residues	2120
Excluded volume	296720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rhq__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 (5)

Entity 1 Entity 1 polymer

Description description	Phenylalanyl-tRNA synthetase alpha chain
Molecular weight formula_weight	33395.8 kDa
EC 编号 ec_number	6.1.1.20
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	8715

MGSSHHHHHHSSGLVPRGSHMGTELMEKLNQQLAEETIDVTLPSRQISIGSKHPLTRTVEEIEDLFLGLGYEIVDGYEVEQDYYNFEALNLPKSHPARDMQDSFYITDEILMRTHTSPVQARTMEKRNGQGPVKIICPGKVYRRDSDDATHSHQFTQIEGLVVDKNIKMSDLKGTLELVAKKLFGADREIRLRPSYFPFTEPSVEVDVSCFKCKGKGCNVCKHTGWIEILGAGMVHPNVLEMAGFDSNEYSGFAFGMGPDRIAMLKYGIEDIRYFYTNDVRFLEQFKAVEDRGE

Source Source

Source organism organism	Staphylococcus haemolyticus
NCBI taxonomy ID ncbi_taxonomy_id	1283
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Phenylalanyl-tRNA synthetase beta chain
Molecular weight formula_weight	88207.2 kDa
EC 编号 ec_number	6.1.1.20
Mutation mutation	D34N, D58G, A59S, D60G, Q144P, Q795E
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MLISNEWLKDYVDAGVKVEDLAERITRTGIEVDNMIDYSKDIKNLVVGYIQSKEKGSGNICQVDIGEEEPVQIVCGAPNVDAGQHVIVAKVGGRLPGGIKIKRAKLRGERSEGMICSLQEIGISSNVVPKAYENGIFVFPTEVEPGTDALTALYLNDQVMEFDLTPNRADALSMVGTAYEVAALYQTEMTKPETQSNETSESATNELSVTIDNPEKVPYYSARVVKNVSIEPSPIWVQARLIKAGIRPINNVVDISNYVLLEYGQPLHMFDQDHIGSKEIVVRQAKDEETMTTLDNNERKLVDTDIVISNGQEPIALAGVMGGDFSEVTEQTTNVVIEGAIFDPVSIRHTSRRLNLRSEASSRFEKGIATEFVDEAVDRACYLLQELASGEVLQDRVSSGDLGSFVTPIDITAEKVNKTIGFNLSNDEIQSIFRQLGFETTLKGETLTVNVPSRRKDITIKEDLIEEVARIYGYDEIPSSLPVFGEVTSGELTDRQHKTRTLKETLEGAGLNQAITYSLVSKDHAKDFALQERPTISLLMPMSEAHATLRQSLLPHLIEATAYNVARKNKDVRLYEIGRVFFGNGEGELPDEVEYLSGILTGEYVVNAWQGKKEEIDFFIAKGVVDRVAEKLNLEFSYKAGKIEGLHPGRTAIVSLEGQDIGFIGELHPQVAADNDLKRTYVFELNYDAMMQVAVGYINYEQIPKFPGVTRDIALEVNHDVPSSELKQIIHNNGEDILQSTLVFDVYEGEHLEKGKKSVAIRLNYLDTEDTLTDERVSKIHDKILEALQAEGATI

Source Source

Source organism organism	Staphylococcus haemolyticus
NCBI taxonomy ID ncbi_taxonomy_id	1283
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1-{3-[(4-pyridin-2-ylpiperazin-1-yl)sulfonyl]phenyl}-3-(1,3-thiazol-2-yl)urea
Molecular weight formula_weight	444.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	349

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2rhqa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.0 — automated matches

Domain ID domain_id	d2rhqa2
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 (7 domains)

Domain ID domain_id	2rhqA00
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	2rhqB01
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	2rhqB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2rhqB03
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	2rhqB04
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	2rhqB05
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	2rhqB06
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	380 — Ferrodoxin-fold anticodon-binding domain

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Unit-cell length a length_a	249.312 Å
Unit-cell length b length_b	87.602 Å
Unit-cell length c length_c	61.072 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	35.600 Å
R factor r_factor	0.2000
R_work r_work	0.1960
R_free r_free	0.2690

PheRS from Staphylococcus haemolyticus- rational protein engineering and inhibitor studies

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

Phenylalanyl-tRNA synthetase alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

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

2rhq__assembly_1__model_1

2rhq__assembly_1__model_1 | I(q)

2rhq__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (2 domains)

CATH v4.4 (7 domains)

7. Citations (1)

PheRS from Staphylococcus haemolyticus- rational protein engineering and inhibitor studies

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

Phenylalanyl-tRNA synthetase alpha 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

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

2rhq__assembly_1__model_1

2rhq__assembly_1__model_1 | I(q)

2rhq__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (2 domains)

CATH v4.4 (7 domains)

7. Citations (1)