SAXSdb — 2nre

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

tRNA pseudouridine synthase A

Escherichia coli K12

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 Homooligomer Protein × 2 RNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 7–270	Not recorded	leucyl tRNA × 2 K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20% PEG 3350, 0.2 M K3 Citrate, 5 mM spermine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.00 Å R-free 0.357

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 2NRE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DJ0 THE CRYSTAL STRUCTURE OF E. COLI PSEUDOURIDINE SYNTHASE I AT 1.5 ANGSTROM RESOLUTION Deposited 1999-11-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 7–270（264 aa） Chain B 7–270（264 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 6.5；298 K；MES BUFFER, pH 6.5, MICRODIALYSIS, temperature 298K	Resolution 1.50 Å R-free 0.221
2NQP Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA Deposited 2006-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain C 7–270（264 aa） Chain D 7–270（264 aa）	Not recorded	K POTASSIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG 3350, 0.2 M K3 Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.279
2NQP Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA Deposited 2006-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 7–270（264 aa） Chain B 7–270（264 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG 3350, 0.2 M K3 Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.279
2NR0 Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA Deposited 2006-11-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 7–270（264 aa） Chain B 7–270（264 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG 3350, 0.2 M K3 Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.90 Å R-free 0.350
2NR0 Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA Deposited 2006-11-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 7–270（264 aa） Chain D 7–270（264 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG 3350, 0.2 M K3 Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.90 Å R-free 0.350

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRUA_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 7–270； UniProt 7–270

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	2nre
Deposition date deposition_date	2006-11-01
Structure title title	Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA
Keywords keywords	pseudouridine synthase, anticodon stem loop, tRNA, multisite specificity, ISOMERASE-RNA COMPLEX; ISOMERASE/RNA
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	25.56 Å
Radius of gyration Rg (electron density) rg_electron	25.09 Å
Forward intensity I(0) i0	57424500.00
Molecular weight molecular_weight	45935.0 kDa
Excluded volume excluded_volume	51716 Å³
Envelope volume envelope_volume	70837 Å³
Hydration-shell volume shell_volume	24872 Å³
Envelope diameter envelope_diameter	90.8 Å
Shell Rg shell_rg	30.89 Å
Envelope Rg envelope_rg	24.93 Å
Shape Rg shape_rg	25.00 Å
Total Rg total_rg	25.80 Å
Total atoms total_atoms	3159
Residues n_residues	314
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	88.1 Å
Rg (real space) rg_real	25.64 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	5.7420e+07
I(0) uncertainty (real space) i0_real_error	8.5350e+05
Rg (reciprocal space) rg_reciprocal	25.62 Å
I(0) (reciprocal space) i0_reciprocal	57420000.0000
Solution quality estimate total_estimate	0.8750
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.4 Å
Skewness Skewness skewness	0.452
Kurtosis Kurtosis kurtosis	-0.126
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4963000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.979

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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	leucyl tRNA
Molecular weight formula_weight	28094.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	F
Atom count atom_count	3159

GCCGAGGUGGUGGAAUUGGUAGACACGCUACCUUGAGGUGGUAGUGCCCAAUAGGGCUUACGGGUUCAAGUCCCGUCCUCGGUACCA

Entity 2 Entity 2 polymer

Description description	tRNA pseudouridine synthase A
Molecular weight formula_weight	30441.6 kDa
EC 编号 ec_number	5.4.99.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MSDQQQPPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPDRYDLPKPPMGPLFLAD

来源 Source

来源生物 organism	Escherichia coli K12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2nrea1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.265 — Pseudouridine synthase
Superfamily Superfamily superfamily	d.265.1 — Pseudouridine synthase
Family Family family	d.265.1.1 — Pseudouridine synthase I TruA

CATH v4.4 (2 domains)

Domain ID domain_id	2nreA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	580 — Pseudouridine synthase I, catalytic domain, N-terminal subdomain

Domain ID domain_id	2nreA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	660 — Pseudouridine synthase I, catalytic domain, C-terminal subdomain

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8. Citations (1)

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Unit-cell length a length_a	80.355 Å
Unit-cell length b length_b	80.355 Å
Unit-cell length c length_c	205.373 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	4.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2646
R_work r_work	0.2595
R_free r_free	0.3574

fit	/app/data/saxs_computation/nr/2nre/2nre.fit
pddf	/app/data/pr_computation/nr/2nre/2nre.pr.out
profile	/app/data/saxs_computation/nr/2nre/2nre.dat

Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA

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

tRNA pseudouridine synthase A

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)