SAXSdb — 2nqp

▼

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 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain C； UniProt 7–270 Chain D； UniProt 7–270	Not recorded	transfer RNA × 1 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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 7–270 Chain B； UniProt 7–270	Not recorded	No other associated polymer	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

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 2NQP	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 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
2NR0 Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA Deposited 2006-11-01	Different oligomeric state 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 oligomeric state 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
2NRE Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA Deposited 2006-11-01	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: tetrameric	Chain A 7–270（264 aa）	Not recorded	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

3 other PDB entries and 4 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 Author chain B； PDBConstruct 7–270； UniProt 7–270 Author chain C； PDBConstruct 7–270； UniProt 7–270 Author chain D； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2nqp
Deposition date deposition_date	2006-10-31
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

▼

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

Radius of gyration Rg (Guinier) rg_guinier	37.07 Å
Radius of gyration Rg (electron density) rg_electron	38.14 Å
Forward intensity I(0) i0	369921000.00
Molecular weight molecular_weight	139870.0 kDa
Excluded volume excluded_volume	167920 Å³
Envelope volume envelope_volume	224840 Å³
Hydration-shell volume shell_volume	51102 Å³
Envelope diameter envelope_diameter	134.5 Å
Shell Rg shell_rg	42.35 Å
Envelope Rg envelope_rg	37.25 Å
Shape Rg shape_rg	38.21 Å
Total Rg total_rg	38.17 Å
Total atoms total_atoms	9765
Residues n_residues	1119
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

▼

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

Maximum dimension Dmax dmax	129.2 Å
Rg (real space) rg_real	37.19 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	3.6990e+08
I(0) uncertainty (real space) i0_real_error	6.4240e+06
Rg (reciprocal space) rg_reciprocal	37.12 Å
I(0) (reciprocal space) i0_reciprocal	369900000.0000
Solution quality estimate total_estimate	0.8491
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	45.1 Å
Skewness Skewness skewness	0.496
Kurtosis Kurtosis kurtosis	-0.042
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	38950000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.735; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.875

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	transfer RNA
Molecular weight formula_weight	28075.7 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	9765

GCCCGGAUGGUGGAAUCGGUAGACACAAGGGAUUAAAAAUCCCUCGGCGUUCGCGCUGUGCGGGUUCAAGUCCCGCUCCGGGUACCA

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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D

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	6

▼

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2nqpa1
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

Domain ID domain_id	d2nqpb1
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

Domain ID domain_id	d2nqpc1
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

Domain ID domain_id	d2nqpd1
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 (8 domains)

Domain ID domain_id	2nqpA01
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	2nqpA02
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

Domain ID domain_id	2nqpB01
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	2nqpB02
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

Domain ID domain_id	2nqpC01
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	2nqpC02
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

Domain ID domain_id	2nqpD01
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	2nqpD02
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	96.278 Å
Unit-cell length b length_b	128.585 Å
Unit-cell length c length_c	159.256 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2494
R_work r_work	0.2460
R_free r_free	0.2791

fit	/app/data/saxs_computation/nq/2nqp/2nqp.fit
pddf	/app/data/pr_computation/nq/2nqp/2nqp.pr.out
profile	/app/data/saxs_computation/nq/2nqp/2nqp.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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)