SAXSdb — 1bu8

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

PROTEIN (PANCREATIC LIPASE RELATED PROTEIN 2)

Rattus norvegicus

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 17–468	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.4；PROTEIN WAS CRYSTALLIZED FROM 8% PEG 8000 WITH 0.1 M TRIS/HCL PH 8.4	Resolution 1.80 Å R-free 0.244

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	LIP2_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–452； UniProt 17–468

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	1bu8
Deposition date deposition_date	1998-09-14
Structure title title	RAT PANCREATIC LIPASE RELATED PROTEIN 2
Keywords keywords	HYDROLASE, LIPID DEGRADATION, PANCREATIC LIPASE; 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	25.32 Å
Radius of gyration Rg (electron density) rg_electron	25.05 Å
Forward intensity I(0) i0	42642800.00
Molecular weight molecular_weight	50165.0 kDa
Excluded volume excluded_volume	62470 Å³
Envelope volume envelope_volume	72613 Å³
Hydration-shell volume shell_volume	25447 Å³
Envelope diameter envelope_diameter	93.1 Å
Shell Rg shell_rg	30.72 Å
Envelope Rg envelope_rg	25.52 Å
Shape Rg shape_rg	25.02 Å
Total Rg total_rg	25.75 Å
Total atoms total_atoms	3532
Residues n_residues	446
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	89.0 Å
Rg (real space) rg_real	25.49 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	4.2640e+07
I(0) uncertainty (real space) i0_real_error	5.7850e+05
Rg (reciprocal space) rg_reciprocal	25.43 Å
I(0) (reciprocal space) i0_reciprocal	42640000.0000
Solution quality estimate total_estimate	0.8291
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.8 Å
Skewness Skewness skewness	0.594
Kurtosis Kurtosis kurtosis	-0.062
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11050000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.674; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.774; 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	PROTEIN (PANCREATIC LIPASE RELATED PROTEIN 2)
Molecular weight formula_weight	50920.4 kDa
EC 编号 ec_number	3.1.1.3
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	3827

KEVCYGHLGCFSNDKPWAGMLQRPLKIFPWSPEDIDTRFLLYTNENPNNYQKISATEPDTIKFSNFQLDRKTRFIVHGFIDKGEDGWLLDMCKKMFQVEKVNCICVDWRRGSRTEYTQASYNTRVVGAEIAFLVQVLSTEMGYSPENVHLIGHSLGAHVVGEAGRRLEGHVGRITGLDPAEPCFQGLPEEVRLDPSDAMFVDVIHTDSAPIIPYLGFGMSQKVGHLDFFPNGGKEMPGCQKNILSTIVDINGIWEGTQNFVACNHLRSYKYYASSILNPDGFLGYPCSSYEKFQQNDCFPCPEEGCPKMGHYADQFEGKTATVEQTVYLNTGDSGNFTRWRYKVSVTLSGAKKLSGYILVALYGNNGNSKQYEIFKGSLKPEARHVRDIDVDINVGEIQKVKFLWNNKVINLFRPTLGASQITVQSGVDGKEYNFCSSDTVREDVLQSLYPC

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
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	295

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bu8a1
Class class	b — All beta proteins
Fold Fold fold	b.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Superfamily Superfamily superfamily	b.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Family Family family	b.12.1.2 — Colipase-binding domain

Domain ID domain_id	d1bu8a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.19 — Pancreatic lipase, N-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	1bu8A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	1bu8A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	60 — Lipoxygenase-1
Homologous superfamily homologous superfamily	20 — PLAT/LH2 domain

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8. Citations (1)

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Unit-cell length a length_a	57.393 Å
Unit-cell length b length_b	79.133 Å
Unit-cell length c length_c	60.940 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.07 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2020
R_work r_work	0.2020
R_free r_free	0.2440

fit	/app/data/saxs_computation/bu/1bu8/1bu8.fit
pddf	/app/data/pr_computation/bu/1bu8/1bu8.pr.out
profile	/app/data/saxs_computation/bu/1bu8/1bu8.dat

RAT PANCREATIC LIPASE RELATED PROTEIN 2

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

PROTEIN (PANCREATIC LIPASE RELATED PROTEIN 2)

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