SAXSdb — 1b65

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

PROTEIN (AMINOPEPTIDASE)

Ochrobactrum anthropi

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–375 Chain B； UniProt 1–375 Chain C； UniProt 1–375 Chain D； UniProt 1–375	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 9；pH 9.0	Resolution 1.82 Å R-free 0.206
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 1–375 Chain F； UniProt 1–375	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 9；pH 9.0	Resolution 1.82 Å R-free 0.206

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q59632_OCHAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–375； UniProt 1–375 Author chain B； PDBConstruct 1–375； UniProt 1–375 Author chain C； PDBConstruct 1–375； UniProt 1–375 Author chain D； PDBConstruct 1–375； UniProt 1–375 Author chain E； PDBConstruct 1–375； UniProt 1–375 Author chain F； PDBConstruct 1–375； UniProt 1–375

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	1b65
Deposition date deposition_date	1999-01-20
Structure title title	Structure of l-aminopeptidase d-ala-esterase/amidase from ochrobactrum anthropi, a prototype for the serine aminopeptidases, reveals a new variant among the ntn hydrolase fold
Keywords keywords	HYDROLASE, PEPTIDE DEGRADATION, NTN HYDROLASE; HYDROLASE
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	41.63 Å
Radius of gyration Rg (electron density) rg_electron	41.25 Å
Forward intensity I(0) i0	855970000.00
Molecular weight molecular_weight	234100.0 kDa
Excluded volume excluded_volume	290150 Å³
Envelope volume envelope_volume	365760 Å³
Hydration-shell volume shell_volume	72167 Å³
Envelope diameter envelope_diameter	150.0 Å
Shell Rg shell_rg	47.90 Å
Envelope Rg envelope_rg	41.44 Å
Shape Rg shape_rg	41.26 Å
Total Rg total_rg	41.54 Å
Total atoms total_atoms	16482
Residues n_residues	2178
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	141.1 Å
Rg (real space) rg_real	41.67 Å
Rg uncertainty (real space) rg_real_error	1.13 Å
I(0) (real space) i0_real	8.5600e+08
I(0) uncertainty (real space) i0_real_error	1.5350e+07
Rg (reciprocal space) rg_reciprocal	41.63 Å
I(0) (reciprocal space) i0_reciprocal	855900000.0000
Solution quality estimate total_estimate	0.6430
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	48.3 Å
Skewness Skewness skewness	0.408
Kurtosis Kurtosis kurtosis	-0.253
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	179100000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 0.008; Positv: 1.000; Valcen: 1.000; Smooth: 0.846

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1b65a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.154 — DmpA/ArgJ-like
Superfamily Superfamily superfamily	d.154.1 — DmpA/ArgJ-like
Family Family family	d.154.1.1 — DmpA-like

Domain ID domain_id	d1b65b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.154 — DmpA/ArgJ-like
Superfamily Superfamily superfamily	d.154.1 — DmpA/ArgJ-like
Family Family family	d.154.1.1 — DmpA-like

Domain ID domain_id	d1b65c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.154 — DmpA/ArgJ-like
Superfamily Superfamily superfamily	d.154.1 — DmpA/ArgJ-like
Family Family family	d.154.1.1 — DmpA-like

Domain ID domain_id	d1b65d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.154 — DmpA/ArgJ-like
Superfamily Superfamily superfamily	d.154.1 — DmpA/ArgJ-like
Family Family family	d.154.1.1 — DmpA-like

Domain ID domain_id	d1b65e_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.154 — DmpA/ArgJ-like
Superfamily Superfamily superfamily	d.154.1 — DmpA/ArgJ-like
Family Family family	d.154.1.1 — DmpA-like

Domain ID domain_id	d1b65f_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.154 — DmpA/ArgJ-like
Superfamily Superfamily superfamily	d.154.1 — DmpA/ArgJ-like
Family Family family	d.154.1.1 — DmpA-like

CATH v4.4 (6 domains)

Domain ID domain_id	1b65A00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	70 — L-amino peptidase D-ALA esterase/amidase
Homologous superfamily homologous superfamily	12 — L-amino peptidase D-ALA esterase/amidase

Domain ID domain_id	1b65B00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	70 — L-amino peptidase D-ALA esterase/amidase
Homologous superfamily homologous superfamily	12 — L-amino peptidase D-ALA esterase/amidase

Domain ID domain_id	1b65C00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	70 — L-amino peptidase D-ALA esterase/amidase
Homologous superfamily homologous superfamily	12 — L-amino peptidase D-ALA esterase/amidase

Domain ID domain_id	1b65D00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	70 — L-amino peptidase D-ALA esterase/amidase
Homologous superfamily homologous superfamily	12 — L-amino peptidase D-ALA esterase/amidase

Domain ID domain_id	1b65E00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	70 — L-amino peptidase D-ALA esterase/amidase
Homologous superfamily homologous superfamily	12 — L-amino peptidase D-ALA esterase/amidase

Domain ID domain_id	1b65F00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	70 — L-amino peptidase D-ALA esterase/amidase
Homologous superfamily homologous superfamily	12 — L-amino peptidase D-ALA esterase/amidase

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8. Citations (3)

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Unit-cell length a length_a	156.970 Å
Unit-cell length b length_b	96.220 Å
Unit-cell length c length_c	154.410 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	24

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

Resolution resolution	1.820 Å
Low-resolution limit resolution_low	12.500 Å
R factor r_factor	0.1700
R_work r_work	0.1690
R_free r_free	0.2060

Description description	PROTEIN (AMINOPEPTIDASE)
Molecular weight formula_weight	40457.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	17786

Structure of l-aminopeptidase d-ala-esterase/amidase from ochrobactrum anthropi, a prototype for the serine aminopeptidases, reveals a new variant among the ntn hydrolase fold

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

PROTEIN (AMINOPEPTIDASE)

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Ochrobactrum anthropi
NCBI Class编号 ncbi_taxonomy_id	529
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1304

fit	/app/data/saxs_computation/b6/1b65/1b65.fit
pddf	/app/data/pr_computation/b6/1b65/1b65.pr.out
profile	/app/data/saxs_computation/b6/1b65/1b65.dat