SAXSdb — 1dbu

▼

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

cysteinyl-tRNA(Pro) deacylase

Haemophilus influenzae

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–158	Non-standard monomer：Yes (specific site not provided by mmCIF)	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.80 Å R-free 0.262

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 1DBU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DBX Crystal structure of cysteinyl-tRNA(Pro) deacylase from H. influenzae (HI1434) Deposited 1999-11-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–158（158 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.259
1DBX Crystal structure of cysteinyl-tRNA(Pro) deacylase from H. influenzae (HI1434) Deposited 1999-11-03	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–158（158 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.259

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

View Construct and Data Evidence

UniProt name	Y1434_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 1–158

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	1dbu
Deposition date deposition_date	1999-11-03
Structure title title	Crystal structure of cysteinyl-tRNA(Pro) deacylase protein from H. influenzae (HI1434)
Keywords keywords	STRUCTURAL GENOMICS, YBAK, Structure 2 Function Project, S2F, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	16.01 Å
Radius of gyration Rg (electron density) rg_electron	14.83 Å
Forward intensity I(0) i0	5391840.00
Molecular weight molecular_weight	16739.0 kDa
Excluded volume excluded_volume	20976 Å³
Envelope volume envelope_volume	24261 Å³
Hydration-shell volume shell_volume	13721 Å³
Envelope diameter envelope_diameter	52.4 Å
Shell Rg shell_rg	20.83 Å
Envelope Rg envelope_rg	15.22 Å
Shape Rg shape_rg	14.84 Å
Total Rg total_rg	15.99 Å
Total atoms total_atoms	1157
Residues n_residues	150
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	51.1 Å
Rg (real space) rg_real	15.90 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	5.3920e+06
I(0) uncertainty (real space) i0_real_error	6.7480e+04
Rg (reciprocal space) rg_reciprocal	15.91 Å
I(0) (reciprocal space) i0_reciprocal	5392000.0000
Solution quality estimate total_estimate	0.8091
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.7 Å
Skewness Skewness skewness	0.120
Kurtosis Kurtosis kurtosis	-0.402
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1184000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	cysteinyl-tRNA(Pro) deacylase
Molecular weight formula_weight	17273.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1359

MTPAIDLLKKQKIPFILHTYDHDPNNQHFGDEAAEKLGIDPNRSFKTLLVAENGDQKKLACFVLATANMLNLKKAAKSIGVKKVEMADKDAAQKSTGYLVGGISPLGQKKRVKTVINSTALEFETIYVSGGKRGLSVEIAPQDLAKVLGAEFTDIVDE

来源 Source

来源生物 organism	Haemophilus influenzae
NCBI Class编号 ncbi_taxonomy_id	727
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1dbua_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.116 — YbaK/ProRS associated domain
Superfamily Superfamily superfamily	d.116.1 — YbaK/ProRS associated domain
Family Family family	d.116.1.1 — YbaK/ProRS associated domain

CATH v4.4 (1 domains)

Domain ID domain_id	1dbuA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	960 — YbaK protein
Homologous superfamily homologous superfamily	10 — YbaK/aminoacyl-tRNA synthetase-associated domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	102.570 Å
Unit-cell length b length_b	42.490 Å
Unit-cell length c length_c	32.540 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.17 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1930
R_free r_free	0.2620

fit	/app/data/saxs_computation/db/1dbu/1dbu.fit
pddf	/app/data/pr_computation/db/1dbu/1dbu.pr.out
profile	/app/data/saxs_computation/db/1dbu/1dbu.dat

Crystal structure of cysteinyl-tRNA(Pro) deacylase protein from H. influenzae (HI1434)

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

cysteinyl-tRNA(Pro) deacylase

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