SAXSdb — 1pys

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

PHENYLALANYL-TRNA SYNTHETASE

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–350	Not recorded	PHENYLALANYL-TRNA SYNTHETASE × 2 （Q5SGX1） MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.7；277 K；PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULFATE 28% OF SATURATION, 20 MM IMIDAZOLE, PH 7.7, 10 MM MGCL2, 1 MM NAN3 AT 4 DEGREES CELSIUS, temperature 277K	Resolution 2.90 Å R-free 0.236

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1PYS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EIY THE CRYSTAL STRUCTURE OF PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH COGNATE TRNAPHE Deposited 2000-02-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–785（785 aa） Fragment：BETA CHAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；ammonium sulphate, magnesium sulphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 3.30 Å R-free 0.287
1JJC Crystal structure at 2.6A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese Deposited 2001-07-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–350（350 aa） Fragment：ALPHA CHAIN	Not recorded	FA5 ADENOSINE-5'-[PHENYLALANINYL-PHOSPHATE] × 2 MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；(NH4)2SO4, Imidazole-HCl, ATP, L-phenylalanine, MnSO4, pH 7.8, VAPOR DIFFUSION, HANGING DROP at 277K	Resolution 2.60 Å R-free 0.258

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q5SGX2_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–350； UniProt 1–350

PHENYLALANYL-TRNA SYNTHETASE

OrganismNot specified

UniProt Q5SGX1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–785	Not recorded	PHENYLALANYL-TRNA SYNTHETASE × 2 （Q5SGX2） MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.7；277 K；PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULFATE 28% OF SATURATION, 20 MM IMIDAZOLE, PH 7.7, 10 MM MGCL2, 1 MM NAN3 AT 4 DEGREES CELSIUS, temperature 277K	Resolution 2.90 Å R-free 0.236

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1PYS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EIY THE CRYSTAL STRUCTURE OF PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH COGNATE TRNAPHE Deposited 2000-02-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain C 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；ammonium sulphate, magnesium sulphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 3.30 Å R-free 0.287
1JJC Crystal structure at 2.6A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese Deposited 2001-07-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–785（785 aa） Fragment：BETA CHAIN	Not recorded	FA5 ADENOSINE-5'-[PHENYLALANINYL-PHOSPHATE] × 2 MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；(NH4)2SO4, Imidazole-HCl, ATP, L-phenylalanine, MnSO4, pH 7.8, VAPOR DIFFUSION, HANGING DROP at 277K	Resolution 2.60 Å R-free 0.258

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q5SGX1_THET8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–785； UniProt 1–785

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	1pys
Deposition date deposition_date	1996-11-14
Structure title title	PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS
Keywords keywords	;PHENYLALANYL-TRNA SYNTHETASE, CLASS II AMINOACYL-TRNA SYNTHETASE, THERMUS THERMOPHILUS, RBD DOMAIN, SH3 DOMAIN, HELIX-TURN-HELIX MOTIF, AMINOACYL-TRNA SYNTHETASE ;; AMINOACYL-TRNA SYNTHETASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	38.78 Å
Radius of gyration Rg (electron density) rg_electron	38.94 Å
Forward intensity I(0) i0	195394000.00
Molecular weight molecular_weight	116530.0 kDa
Excluded volume excluded_volume	147350 Å³
Envelope volume envelope_volume	200600 Å³
Hydration-shell volume shell_volume	45273 Å³
Envelope diameter envelope_diameter	141.9 Å
Shell Rg shell_rg	41.77 Å
Envelope Rg envelope_rg	39.60 Å
Shape Rg shape_rg	38.92 Å
Total Rg total_rg	39.17 Å
Total atoms total_atoms	9972
Residues n_residues	1051
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	142.0 Å
Rg (real space) rg_real	39.25 Å
Rg uncertainty (real space) rg_real_error	1.89 Å
I(0) (real space) i0_real	1.9540e+08
I(0) uncertainty (real space) i0_real_error	3.9770e+06
Rg (reciprocal space) rg_reciprocal	38.96 Å
I(0) (reciprocal space) i0_reciprocal	195300000.0000
Solution quality estimate total_estimate	0.8122
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.1 Å
Skewness Skewness skewness	0.622
Kurtosis Kurtosis kurtosis	-0.011
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	39450000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.661; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.779; Smooth: 0.793

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PHENYLALANYL-TRNA SYNTHETASE
Molecular weight formula_weight	39309.2 kDa
EC 编号 ec_number	6.1.1.20
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10968

MLEEALAAIQNARDLEELKALKARYLGKKGLLTQEMKGLSALPLEERRKRGQELNAIKAALEAALEAREKALEEAALKEALERERVDVSLPGASLFSGGLHPITLMERELVEIFRALGYQAVEGPEVESEFFNFDALNIPEHHPARDMWDTFWLTGEGFRLEGPLGEEVEGRLLLRTHTSPMQVRYMVAHTPPFRIVVPGRVFRFEQTDATHEAVFHQLEGLVVGEGIAMAHLKGAIYELAQALFGPDSKVRFQPVYFPFVEPGAQFAVWWPEGGKWLELGGAGMVHPKVFQAVDAYRERLGLPPAYRGVTGFAFGLGVERLAMLRYGIPDIRYFFGGRLKFLEQFKGVL

Entity 2 Entity 2 polymer

Description description	PHENYLALANYL-TRNA SYNTHETASE
Molecular weight formula_weight	86720.7 kDa
EC 编号 ec_number	6.1.1.20
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MRVPFSWLKAYVPELESPEVLEERLAGLGFETDRIERVFPIPRGVVFARVLEAHPIPGTRLKRLVLDAGRTVEVVSGAENARKGIGVALALPGTELPGLGQKVGERVIQGVRSFGMALSPRELGVGEYGGGLLEFPEDALPPGTPLSEAWPEEVVLDLEVTPNRPDALGLLGLARDLHALGYALVEPEAALKAEALPLPFALKVEDPEGAPHFTLGYAFGLRVAPSPLWMQRALFAAGMRPINNVVDVTNYVMLERAQPMHAFDLRFVGEGIAVRRAREGERLKTLDGVERTLHPEDLVIAGWRGEESFPLGLAGVMGGAESEVREDTEAIALEVACFDPVSIRKTARRHGLRTEASHRFERGVDPLGQVPAQRRALSLLQALAGARVAEALLEAGSPKPPEAIPFRPEYANRLLGTSYPEAEQIAILKRLGCRVEGEGPTYRVTPPSHRLDLRLEEDLVEEVARIQGYETIPLALPAFFPAPDNRGVEAPYRKEQRLREVLSGLGFQEVYTYSFMDPEDARRFRLDPPRLLLLNPLAPEKAALRTHLFPGLVRVLKENLDLDRPERALLFEVGRVFREREETHLAGLLFGEGVGLPWAKERLSGYFLLKGYLEALFARLGLAFRVEAQAFPFLHPGVSGRVLVEGEEVGFLGALHPEIAQELELPPVHLFELRLPLPDKPLAFQDPSRHPAAFRDLAVVVPAPTPYGEVEALVREAAGPYLESLALFDLYQGPPLPEGHKSLAFHLRFRHPKRTLRDEEVEEAVSRVAEALRARGFGLRGLDTP

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	332

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d1pysa_
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.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

Domain ID domain_id	d1pysb1
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.1 — Domains B1 and B5 of PheRS-beta, PheT

Domain ID domain_id	d1pysb2
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.1 — Domains B1 and B5 of PheRS-beta, PheT

Domain ID domain_id	d1pysb3
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.4 — Myf domain

Domain ID domain_id	d1pysb4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.13 — Anticodon-binding domain of PheRS
Family Family family	d.58.13.1 — Anticodon-binding domain of PheRS

Domain ID domain_id	d1pysb5
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.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

Domain ID domain_id	d1pysb6
Class class	b — All beta proteins
Fold Fold fold	b.153 — PheT/TilS domain
Superfamily Superfamily superfamily	b.153.1 — PheT/TilS domain
Family Family family	b.153.1.1 — B3/B4 domain of PheRS, PheT

CATH v4.4 (7 domains)

Domain ID domain_id	1pysA00
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	1pysB01
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	1pysB02
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	1pysB03
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	1pysB04
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	1pysB05
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	1pysB06
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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8. Citations (1)

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Unit-cell length a length_a	176.000 Å
Unit-cell length b length_b	176.000 Å
Unit-cell length c length_c	141.700 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 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1770
R_work r_work	0.1770
R_free r_free	0.2360

fit	/app/data/saxs_computation/py/1pys/1pys.fit
pddf	/app/data/pr_computation/py/1pys/1pys.pr.out
profile	/app/data/saxs_computation/py/1pys/1pys.dat

PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS

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

PHENYLALANYL-TRNA SYNTHETASE

State in the Current Structure

Other States of the Same Protein in the Database

PHENYLALANYL-TRNA SYNTHETASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)