SAXSdb — 1a58

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

CYCLOPHILIN

Brugia malayi

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 1–177	Fragment：CYCLOPHILIN DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；50MM IMIDAZOLE AT PH6.5, 15% SAT. AMMONIUM SULFATE 0.02% SODIUM AZIDE, 0.56 MM PROTEIN CONC.	Resolution 1.95 Å R-free 0.233

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 1A58	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A33 PEPTIDYLPROLYL ISOMERASE, CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI Deposited 1998-01-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–177（177 aa） Fragment：CYCLOPHILIN-LIKE DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；THE INITIAL 6 UL DROP CONSISTED OF 50 MM MES-NAOH PH 6.0, 0.9 M (NH4)2SO4, 1MM PROTEIN. THE 1 ML RESERVOIR SOLUTION CONSISTED OF 100 MM MES-NAOH PH 6.0, 1.8 M (NH4)2SO4	Resolution 2.15 Å R-free 0.211
1C5F CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI COMPLEXED WITH CYCLOSPORIN A Deposited 1999-11-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–177（177 aa） Fragment：CYCLOPHILIN-LIKE DOMAIN, RESIDUES 1-177	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PEG 8000, CALCIUM ACETATE, METHANOL, MES, PH 6.00	Resolution 2.47 Å R-free 0.249
1C5F CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI COMPLEXED WITH CYCLOSPORIN A Deposited 1999-11-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–177（177 aa） Fragment：CYCLOPHILIN-LIKE DOMAIN, RESIDUES 1-177	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PEG 8000, CALCIUM ACETATE, METHANOL, MES, PH 6.00	Resolution 2.47 Å R-free 0.249
1C5F CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI COMPLEXED WITH CYCLOSPORIN A Deposited 1999-11-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–177（177 aa） Fragment：CYCLOPHILIN-LIKE DOMAIN, RESIDUES 1-177	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PEG 8000, CALCIUM ACETATE, METHANOL, MES, PH 6.00	Resolution 2.47 Å R-free 0.249
1C5F CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI COMPLEXED WITH CYCLOSPORIN A Deposited 1999-11-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–177（177 aa） Fragment：CYCLOPHILIN-LIKE DOMAIN, RESIDUES 1-177	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PEG 8000, CALCIUM ACETATE, METHANOL, MES, PH 6.00	Resolution 2.47 Å R-free 0.249
1C5F CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI COMPLEXED WITH CYCLOSPORIN A Deposited 1999-11-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 1–177（177 aa） Fragment：CYCLOPHILIN-LIKE DOMAIN, RESIDUES 1-177	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PEG 8000, CALCIUM ACETATE, METHANOL, MES, PH 6.00	Resolution 2.47 Å R-free 0.249
1C5F CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI COMPLEXED WITH CYCLOSPORIN A Deposited 1999-11-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 1–177（177 aa） Fragment：CYCLOPHILIN-LIKE DOMAIN, RESIDUES 1-177	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PEG 8000, CALCIUM ACETATE, METHANOL, MES, PH 6.00	Resolution 2.47 Å R-free 0.249
1C5F CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI COMPLEXED WITH CYCLOSPORIN A Deposited 1999-11-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 1–177（177 aa） Fragment：CYCLOPHILIN-LIKE DOMAIN, RESIDUES 1-177	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PEG 8000, CALCIUM ACETATE, METHANOL, MES, PH 6.00	Resolution 2.47 Å R-free 0.249
1C5F CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI COMPLEXED WITH CYCLOSPORIN A Deposited 1999-11-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 1–177（177 aa） Fragment：CYCLOPHILIN-LIKE DOMAIN, RESIDUES 1-177	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PEG 8000, CALCIUM ACETATE, METHANOL, MES, PH 6.00	Resolution 2.47 Å R-free 0.249

2 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYP1_BRUMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–177； UniProt 1–177

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	1a58
Deposition date deposition_date	1998-02-20
Structure title title	CYCLOPHILIN FROM BRUGIA MALAYI
Keywords keywords	ISOMERASE, PPIASE; ISOMERASE
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	16.12 Å
Radius of gyration Rg (electron density) rg_electron	15.00 Å
Forward intensity I(0) i0	7226400.00
Molecular weight molecular_weight	19481.0 kDa
Excluded volume excluded_volume	24354 Å³
Envelope volume envelope_volume	26821 Å³
Hydration-shell volume shell_volume	14830 Å³
Envelope diameter envelope_diameter	53.6 Å
Shell Rg shell_rg	21.27 Å
Envelope Rg envelope_rg	15.29 Å
Shape Rg shape_rg	14.95 Å
Total Rg total_rg	16.24 Å
Total atoms total_atoms	1365
Residues n_residues	177
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	52.0 Å
Rg (real space) rg_real	15.99 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	7.2260e+06
I(0) uncertainty (real space) i0_real_error	9.1860e+04
Rg (reciprocal space) rg_reciprocal	16.00 Å
I(0) (reciprocal space) i0_reciprocal	7226000.0000
Solution quality estimate total_estimate	0.8003
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.0 Å
Skewness Skewness skewness	0.074
Kurtosis Kurtosis kurtosis	-0.373
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1679000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a58a_
Class class	b — All beta proteins
Fold Fold fold	b.62 — Cyclophilin-like
Superfamily Superfamily superfamily	b.62.1 — Cyclophilin-like
Family Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

CATH v4.4 (1 domains)

Domain ID domain_id	1a58A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

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8. Citations (1)

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Unit-cell length a length_a	58.215 Å
Unit-cell length b length_b	58.215 Å
Unit-cell length c length_c	141.944 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	24.000 Å
R factor r_factor	0.1990
R_work r_work	0.1990
R_free r_free	0.2330

Description description	CYCLOPHILIN
Molecular weight formula_weight	19504.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1827

CYCLOPHILIN FROM BRUGIA MALAYI

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

CYCLOPHILIN

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

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Brugia malayi
NCBI Class编号 ncbi_taxonomy_id	6279
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	154

fit	/app/data/saxs_computation/a5/1a58/1a58.fit
pddf	/app/data/pr_computation/a5/1a58/1a58.pr.out
profile	/app/data/saxs_computation/a5/1a58/1a58.dat