1ady

HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDYL-ADENYLATE

Method: X-RAY DIFFRACTION D_max: 135.0 Å Quality: GOOD

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

HISTIDYL-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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–421 Chain B； UniProt 1–421	Not recorded	SO4 SULFATE ION × 2 HAM HISTIDYL-ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.	Resolution 2.80 Å R-free 0.300
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–421 Chain D； UniProt 1–421	Not recorded	SO4 SULFATE ION × 2 HAM HISTIDYL-ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.	Resolution 2.80 Å R-free 0.300

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 1ADY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ADJ HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDINE Deposited 1997-02-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–421（421 aa） Chain B 1–421（421 aa）	Not recorded	SO4 SULFATE ION × 2 HIS HISTIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.70 Å R-free 0.277
1ADJ HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDINE Deposited 1997-02-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–421（421 aa） Chain D 1–421（421 aa）	Not recorded	SO4 SULFATE ION × 2 HIS HISTIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.70 Å R-free 0.277
1ADJ HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDINE Deposited 1997-02-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–421（421 aa） Chain B 1–421（421 aa） Chain C 1–421（421 aa） Chain D 1–421（421 aa）	Not recorded	SO4 SULFATE ION × 4 HIS HISTIDINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.70 Å R-free 0.277
1H4V HISTIDYL-TRNA SYNTHETASE from Thermus Thermophilus (ligand free) Deposited 2001-05-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–421（421 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；DESCRIBED IN REFERENCE 1., pH 7.00	Resolution 2.40 Å R-free 0.256

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SYH_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–421； UniProt 1–421 Author chain B； PDBConstruct 1–421； UniProt 1–421 Author chain C； PDBConstruct 1–421； UniProt 1–421 Author chain D； PDBConstruct 1–421； UniProt 1–421

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	1ady
Deposition date deposition_date	1997-02-19
Structure title title	HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDYL-ADENYLATE
Keywords keywords	HISTIDYL-ADENYLATE, AMINO ACID, TRNA SYNTHETASE; 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	40.86 Å
Radius of gyration Rg (electron density) rg_electron	40.88 Å
Forward intensity I(0) i0	545093000.00
Molecular weight molecular_weight	190000.0 kDa
Excluded volume excluded_volume	237610 Å³
Envelope volume envelope_volume	310910 Å³
Hydration-shell volume shell_volume	62891 Å³
Envelope diameter envelope_diameter	140.6 Å
Shell Rg shell_rg	46.42 Å
Envelope Rg envelope_rg	40.68 Å
Shape Rg shape_rg	40.88 Å
Total Rg total_rg	41.16 Å
Total atoms total_atoms	13388
Residues n_residues	1680
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	135.0 Å
Rg (real space) rg_real	40.86 Å
Rg uncertainty (real space) rg_real_error	1.32 Å
I(0) (real space) i0_real	5.4510e+08
I(0) uncertainty (real space) i0_real_error	9.4800e+06
Rg (reciprocal space) rg_reciprocal	40.86 Å
I(0) (reciprocal space) i0_reciprocal	545100000.0000
Solution quality estimate total_estimate	0.8833
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	48.5 Å
Skewness Skewness skewness	0.338
Kurtosis Kurtosis kurtosis	-0.345
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	132700000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.813

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	HISTIDYL-TRNA SYNTHETASE
Molecular weight formula_weight	47125.9 kDa
EC 编号 ec_number	6.1.1.21
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	13388

MTARAVRGTKDLFGKELRMHQRIVATARKVLEAAGALELVTPIFEETQVFEKGVGAATDIVRKEMFTFQDRGGRSLTLRPEGTAAMVRAYLEHGMKVWPQPVRLWMAGPMFRAERPQKGRYRQFHQVNYEALGSENPILDAEAVVLLYECLKELGLRRLKVKLSSVGDPEDRARYNAYLREVLSPHREALSEDSKERLEENPMRILDSKSERDQALLKELGVRPMLDFLGEEARAHLKEVERHLERLSVPYELEPALVRGLDYYVRTAFEVHHEEIGAQSALGGGGRYDGLSELLGGPRVPGVGFAFGVERVALALEAEGFGLPEEKGPDLYLIPLTEEAVAEAFYLAEALRPRLRAEYALAPRKPAKGLEEALKRGAAFAGFLGEDELRAGEVTLKRLATGEQVRLSREEVPGYLLQALG

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	HISTIDYL-ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	484.4 kDa
Source method src_method	syn
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1adya1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
Family Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

Domain ID domain_id	d1adya2
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	d1adyb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
Family Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

Domain ID domain_id	d1adyb2
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	d1adyc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
Family Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

Domain ID domain_id	d1adyc2
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	d1adyd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
Family Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

Domain ID domain_id	d1adyd2
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 (8 domains)

Domain ID domain_id	1adyA01
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	1adyA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	1adyB01
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	1adyB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	1adyC01
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	1adyC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	1adyD01
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	1adyD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

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8. Citations (1)

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Unit-cell length a length_a	171.300 Å
Unit-cell length b length_b	214.700 Å
Unit-cell length c length_c	49.300 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2600
R_work r_work	0.2600
R_free r_free	0.3000

fit	/app/data/saxs_computation/ad/1ady/1ady.fit
pddf	/app/data/pr_computation/ad/1ady/1ady.pr.out
profile	/app/data/saxs_computation/ad/1ady/1ady.dat