2iy5

PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog

Method: X-RAY DIFFRACTION D_max: 176.5 Å Quality: GOOD

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

PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN

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–RNA Heteromer Protein × 4 RNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 1–350	Not recorded	PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN × 2 （P27002） TRNAPHE × 2 FYA ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE] × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；20 MM IMIDAZOLE-HCL, PH 7.8, 1 MM MGCL2, 5 MM 2-MERCAPTOETHANOL AND 1 MM NAN3	Resolution 3.10 Å R-free 0.299

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 2IY5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B70 PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINE Deposited 1999-01-26	Different construct Different oligomeric state 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 SUBUNIT	Not recorded	MG MAGNESIUM ION × 2 PHE PHENYLALANINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；313 K；CRYSTALS WERE GROWN BY THE HANGING-DROP TECHNIQUE AT 4O C WITH AMMONIUM SULFATE AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 M L) AT A PROTEIN CONCENTRTION OF 3 TO 5 MG PER ML IN 20 AMM IMIDASOL-HCL BUFFER (PH 7.8), 1 MM MGCL2, 1 MM NAN3 AND 15% SATURATED AMMONIUM SULFATE WAS EQUILIBRATED WITH 1 ML 25 TO 30% SATURATED AMMONIUM SULFATE IN THE SAME BUFFER. CRYSTALS APPEARED AFTER ONE TO TWO WEEKS AND GREW UP TO MAXIMAL DIMENSIONS (0.4MMX0.4MMX0.25 MM) IN A FEW WEEKS., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 313K	Resolution 2.70 Å R-free 0.256
1B7Y PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE Deposited 1999-01-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–350（350 aa）	Not recorded	MG MAGNESIUM ION × 2 FYA ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE] × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；313 K；HANGING-DROP TECHNIQUE AT 4O C WITH (NH4)2SO4 AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 microliters) AT PROTEIN CONCENTRATION OF 3 TO 5 MG PER ML IN 20 MM IMIDASOL-HCL BUFFER (PH 7.8), 1 MM MGCL2, 1 MM NAN3 AND 15% SATURATED (NH4)2SO4 IN THE SAME BUFFER. CRYSTALS APPEARED AFTER ONE TO TWO WEEKS AND GREW UP TO THE MAXIMAL DIMENSIONS OF 0.4X0.4X0.25 MM IN A FEW WEEKS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 313K	Resolution 2.50 Å R-free 0.267
1EIY THE CRYSTAL STRUCTURE OF PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH COGNATE TRNAPHE Deposited 2000-02-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 1–350（350 aa） Fragment：ALPHA 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
2AKW Crystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase complexed with p-Cl-Phenylalanine Deposited 2005-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 85–350（266 aa）	Not recorded	MN MANGANESE (II) ION × 2 200 4-CHLORO-L-PHENYLALANINE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；20mM Imidazole-HCl (pH 7.2), 27% (NH4)2SO4, 1mM MgCl2, 1mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.234
2ALY Crystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase complexed with 5'-O-[N-(L-tyrosyl)sulphamoyl]adenosine Deposited 2005-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 85–350（266 aa）	Not recorded	MN MANGANESE (II) ION × 2 YSA 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；20mM Imidazole-HCl (pH 7.2), 27% (NH4)2SO4, 1mM MgCl2, 1mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.246
2AMC Crystal structure of Phenylalanyl-tRNA synthetase complexed with L-tyrosine Deposited 2005-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 85–350（266 aa） Fragment：residues 85-350	Not recorded	MG MAGNESIUM ION × 2 TYR TYROSINE × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；20 mM Imidazole-HCl, pH 7.2, 27% (NH4)2SO4, 1mM MgCl2, 1mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.255
3HFZ Crystal structure of Thermus thermophilus Phenylalanyl-tRNA synthetase complexed with m-tyrosine Deposited 2009-05-13	Different oligomeric state 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）	Not recorded	MTY META-TYROSINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；292 K；30% (NH4)2SO4, 0.02M IMIDAZOLE-HCL, 0.001M magnesium chloride, m-tyrosine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.90 Å R-free 0.282
3TEH Crystal structure of Thermus thermophilus Phenylalanyl-tRNA synthetase complexed with L-dopa Deposited 2011-08-14	Different oligomeric state 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）	Not recorded	DAH 3,4-DIHYDROXYPHENYLALANINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；292 K；30% (NH4)2SO4, 0.02M IMIDAZOLE-HCL, 0.001M magnesium chloride, L-dopa, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.85 Å R-free 0.297
4TVA Universal Pathway for Post-Transfer Editing Reactions: Insight from Crystal structure of TthPheRS with Puromycine Deposited 2014-06-26	Different oligomeric state 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）	Not recorded	PHE PHENYLALANINE × 2 PUY PUROMYCIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；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	Resolution 2.60 Å R-free 0.258

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

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

PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN

OrganismNot specified

UniProt P27002

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–RNA Heteromer Protein × 4 RNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain B； UniProt 1–785	Not recorded	PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN × 2 （P27001） TRNAPHE × 2 FYA ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE] × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；20 MM IMIDAZOLE-HCL, PH 7.8, 1 MM MGCL2, 5 MM 2-MERCAPTOETHANOL AND 1 MM NAN3	Resolution 3.10 Å R-free 0.299

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 2IY5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B70 PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINE Deposited 1999-01-26	Different construct Different oligomeric state 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 SUBUNIT	Not recorded	MG MAGNESIUM ION × 2 PHE PHENYLALANINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；313 K；CRYSTALS WERE GROWN BY THE HANGING-DROP TECHNIQUE AT 4O C WITH AMMONIUM SULFATE AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 M L) AT A PROTEIN CONCENTRTION OF 3 TO 5 MG PER ML IN 20 AMM IMIDASOL-HCL BUFFER (PH 7.8), 1 MM MGCL2, 1 MM NAN3 AND 15% SATURATED AMMONIUM SULFATE WAS EQUILIBRATED WITH 1 ML 25 TO 30% SATURATED AMMONIUM SULFATE IN THE SAME BUFFER. CRYSTALS APPEARED AFTER ONE TO TWO WEEKS AND GREW UP TO MAXIMAL DIMENSIONS (0.4MMX0.4MMX0.25 MM) IN A FEW WEEKS., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 313K	Resolution 2.70 Å R-free 0.256
1B7Y PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE Deposited 1999-01-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–785（785 aa）	Not recorded	MG MAGNESIUM ION × 2 FYA ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE] × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；313 K；HANGING-DROP TECHNIQUE AT 4O C WITH (NH4)2SO4 AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 microliters) AT PROTEIN CONCENTRATION OF 3 TO 5 MG PER ML IN 20 MM IMIDASOL-HCL BUFFER (PH 7.8), 1 MM MGCL2, 1 MM NAN3 AND 15% SATURATED (NH4)2SO4 IN THE SAME BUFFER. CRYSTALS APPEARED AFTER ONE TO TWO WEEKS AND GREW UP TO THE MAXIMAL DIMENSIONS OF 0.4X0.4X0.25 MM IN A FEW WEEKS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 313K	Resolution 2.50 Å R-free 0.267
2AKW Crystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase complexed with p-Cl-Phenylalanine Deposited 2005-08-04	Different oligomeric state 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）	Not recorded	MN MANGANESE (II) ION × 2 200 4-CHLORO-L-PHENYLALANINE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；20mM Imidazole-HCl (pH 7.2), 27% (NH4)2SO4, 1mM MgCl2, 1mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.234
2ALY Crystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase complexed with 5'-O-[N-(L-tyrosyl)sulphamoyl]adenosine Deposited 2005-08-04	Different oligomeric state 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）	Not recorded	MN MANGANESE (II) ION × 2 YSA 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；20mM Imidazole-HCl (pH 7.2), 27% (NH4)2SO4, 1mM MgCl2, 1mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.246
2AMC Crystal structure of Phenylalanyl-tRNA synthetase complexed with L-tyrosine Deposited 2005-08-09	Different oligomeric state 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）	Not recorded	MG MAGNESIUM ION × 2 TYR TYROSINE × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；20 mM Imidazole-HCl, pH 7.2, 27% (NH4)2SO4, 1mM MgCl2, 1mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.255
3HFZ Crystal structure of Thermus thermophilus Phenylalanyl-tRNA synthetase complexed with m-tyrosine Deposited 2009-05-13	Different oligomeric state 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）	Not recorded	MTY META-TYROSINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；292 K；30% (NH4)2SO4, 0.02M IMIDAZOLE-HCL, 0.001M magnesium chloride, m-tyrosine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.90 Å R-free 0.282
3TEH Crystal structure of Thermus thermophilus Phenylalanyl-tRNA synthetase complexed with L-dopa Deposited 2011-08-14	Different oligomeric state 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）	Not recorded	DAH 3,4-DIHYDROXYPHENYLALANINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；292 K；30% (NH4)2SO4, 0.02M IMIDAZOLE-HCL, 0.001M magnesium chloride, L-dopa, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.85 Å R-free 0.297
4TVA Universal Pathway for Post-Transfer Editing Reactions: Insight from Crystal structure of TthPheRS with Puromycine Deposited 2014-06-26	Different oligomeric state 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）	Not recorded	PHE PHENYLALANINE × 2 PUY PUROMYCIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；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	Resolution 2.60 Å R-free 0.258

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SYFB_THETH
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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2iy5
Deposition date deposition_date	2006-07-12
Structure title title	PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog
Keywords keywords	;CLASS II AMINOACYL-TRNA SYNTHETASE, LIGASE, RBD DOMIN, MAGNESIUM, SH3 DOMAIN, PHENYLALANYL-TRNA SYNTHETASE, THERMUS THERMOPHILUS, PROTEIN BIOSYNTHESIS, METAL-BINDING, NUCLEOTIDE-BINDING, RNA-BINDING, ATP-BINDING, TRNA-BINDING, HELIX-TURN-HELIX MOTIF, AMINOACYL-TRNA SYNTHETASE ;; LIGASE
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	49.68 Å
Radius of gyration Rg (electron density) rg_electron	48.66 Å
Forward intensity I(0) i0	396887000.00
Molecular weight molecular_weight	148890.0 kDa
Excluded volume excluded_volume	180110 Å³
Envelope volume envelope_volume	280110 Å³
Hydration-shell volume shell_volume	53515 Å³
Envelope diameter envelope_diameter	171.6 Å
Shell Rg shell_rg	45.77 Å
Envelope Rg envelope_rg	48.09 Å
Shape Rg shape_rg	48.47 Å
Total Rg total_rg	49.10 Å
Total atoms total_atoms	10418
Residues n_residues	1193
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	176.5 Å
Rg (real space) rg_real	50.44 Å
Rg uncertainty (real space) rg_real_error	2.19 Å
I(0) (real space) i0_real	3.9690e+08
I(0) uncertainty (real space) i0_real_error	7.5810e+06
Rg (reciprocal space) rg_reciprocal	49.69 Å
I(0) (reciprocal space) i0_reciprocal	396500000.0000
Solution quality estimate total_estimate	0.7815
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.1 Å
Skewness Skewness skewness	0.478
Kurtosis Kurtosis kurtosis	-0.594
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18210000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.632; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.535; Smooth: 0.723

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN
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	10649

MLEEALAAIQNARDLEELKALKARYLGKKGLLTQEMKGLSALPLEERRKRGQELNAIKAALEAALEAREKALEEAALKEALERERVDVSLPGASLFSGGLHPITLMERELVEIFRALGYQAVEGPEVESEFFNFDALNIPEHHPARDMWDTFWLTGEGFRLEGPLGEEVEGRLLLRTHTSPMQVRYMVAHTPPFRIVVPGRVFRFEQTDATHEAVFHQLEGLVVGEGIAMAHLKGAIYELAQALFGPDSKVRFQPVYFPFVEPGAQFAVWWPEGGKWLELGGAGMVHPKVFQAVDAYRERLGLPPAYRGVTGFAFGLGVERLAMLRYGIPDIRYFFGGRLKFLEQFKGVL

Entity 2 Entity 2 polymer

Description description	PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN
Molecular weight formula_weight	86736.7 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

MRVPFSWLKAYVPELESPEVLEERLAGLGFETDRIERVFPIPRGVVFARVLEAHPIPGTRLKRLVLDAGRTVEVVSGAENARKGIGVALALPGTELPGLGQKVGERVIQGVRSFGMALSPRELGVGEYGGGLLEFPEDALPPGTPLSEAWPEEVVLDLEVTPNRPDALGLLGLARDLHALGYALVEPEAALKAEALPLPFALKVEDPEGAPHFTLGYAFGLRVAPSPLWMQRALFAAGMRPINNVVDVTNYVMLERAQPMHAFDLRFVGEGIAVRRAREGERLKTLDGVERTLHPEDLVIAGWRGEESFPLGLAGVMGGAESEVREDTEAIALEVACFDPVSIRKTARRHGLRTEASHRFERGVDPLGQVPAQRRALSLLQALAGARVAEALLEAGSPKPPEAIPFRPEYANRLLGTSYPEAEQIAILKRLGCRVEGEGPTYRVTPPSHRLDLRLEEDLVEEVARIEGYETIPLALPAFFPAPDNRAVEAPYRKEQRLREVLSGLGFQEVYTYSFMDPEDARRFRLDPPRLLLLNPLAPEKAALRTHLFPGLVRVLKENLDLDRPERALLFEVGRVFREREETHLAGLLFGEGVGLPWAKERLSGYFLLKGYLEALFARLGLAFRVEAEAFPFLHPGVSGRVLVEGEEVGFLGALHPEIAQELELPPVHLFELRLPLPDKPLAFQDPSRHPAAFRDLAVVVPAPTPYGEVEALVREAAGPYLESLALFDLYQGPPLPEGHKSLAFHLRFRHPKRTLRDEEVEEAVSRVAEALRARGFGLRGLDTP

Entity 3 Entity 3 polymer

Description description	TRNAPHE
Molecular weight formula_weight	24484.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	T

GCCGAGGUAGCUCAGUUGGUAGAGCAUGCGACUGAAAAUCGCAGUGUCCGCGGUUCGAUUCCGCGCCUCGGCACCA

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE]
Molecular weight formula_weight	480.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	231

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7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2iy5a1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.7 — tRNA-binding arm
Family Family family	a.2.7.2 — Phenylalanyl-tRNA synthetase (PheRS)

Domain ID domain_id	d2iy5a2
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	d2iy5b1
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	d2iy5b2
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	d2iy5b3
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	d2iy5b4
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

Domain ID domain_id	d2iy5b5
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	d2iy5b6
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

CATH v4.4 (7 domains)

Domain ID domain_id	2iy5A00
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	2iy5B01
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	2iy5B02
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	2iy5B03
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	2iy5B04
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	2iy5B05
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	2iy5B06
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	173.400 Å
Unit-cell length b length_b	173.400 Å
Unit-cell length c length_c	139.400 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	3.100 Å
Low-resolution limit resolution_low	9.990 Å
R factor r_factor	0.2380
R_work r_work	0.2380
R_free r_free	0.2990

fit	/app/data/saxs_computation/iy/2iy5/2iy5.fit
pddf	/app/data/pr_computation/iy/2iy5/2iy5.pr.out
profile	/app/data/saxs_computation/iy/2iy5/2iy5.dat

PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog

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

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (8 domains)

CATH v4.4 (7 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)