SAXSdb — 1ci0

▼

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

PROTEIN (PNP OXIDASE)

Saccharomyces cerevisiae

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–228 Chain B； UniProt 1–228	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 2.70 Å R-free 0.274

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	PDX3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–228； UniProt 1–228 Author chain B； PDBConstruct 1–228； UniProt 1–228

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	1ci0
Deposition date deposition_date	1999-04-06
Structure title title	PNP OXIDASE FROM SACCHAROMYCES CEREVISIAE
Keywords keywords	;OXIDASE, B6 METABOLISM, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, OXIDOREDUCTASE ;; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	22.90 Å
Radius of gyration Rg (electron density) rg_electron	21.77 Å
Forward intensity I(0) i0	40299400.00
Molecular weight molecular_weight	48125.0 kDa
Excluded volume excluded_volume	59795 Å³
Envelope volume envelope_volume	69200 Å³
Hydration-shell volume shell_volume	26114 Å³
Envelope diameter envelope_diameter	85.1 Å
Shell Rg shell_rg	29.30 Å
Envelope Rg envelope_rg	22.23 Å
Shape Rg shape_rg	21.75 Å
Total Rg total_rg	22.72 Å
Total atoms total_atoms	3409
Residues n_residues	409
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	81.5 Å
Rg (real space) rg_real	22.84 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	4.0300e+07
I(0) uncertainty (real space) i0_real_error	5.4830e+05
Rg (reciprocal space) rg_reciprocal	22.85 Å
I(0) (reciprocal space) i0_reciprocal	40300000.0000
Solution quality estimate total_estimate	0.8491
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.8 Å
Skewness Skewness skewness	0.340
Kurtosis Kurtosis kurtosis	-0.100
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9219000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.683; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.999

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN (PNP OXIDASE)
Molecular weight formula_weight	26949.3 kDa
EC 编号 ec_number	1.4.3.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3441

MTKQAEETQKPIIFAPETYQYDKFTLNEKQLTDDPIDLFTKWFNEAKEDPRETLPEAITFSSAELPSGRVSSRILLFKELDHRGFTIYSNWGTSRKAHDIATNPNAAIVFFWKDLQRQVRVEGITEHVNRETSERYFKTRPRGSKIGAWASRQSDVIKNREELDELTQKNTERFKDAEDIPCPDYWGGLRIVPLEIEFWQGRPSRLHDRFVYRRKTENDPWKVVRLAP

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	32

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ci0a_
Class class	b — All beta proteins
Fold Fold fold	b.45 — Split barrel-like
Superfamily Superfamily superfamily	b.45.1 — FMN-binding split barrel
Family Family family	b.45.1.1 — PNP-oxidase like

Domain ID domain_id	d1ci0b_
Class class	b — All beta proteins
Fold Fold fold	b.45 — Split barrel-like
Superfamily Superfamily superfamily	b.45.1 — FMN-binding split barrel
Family Family family	b.45.1.1 — PNP-oxidase like

CATH v4.4 (2 domains)

Domain ID domain_id	1ci0A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Electron Transport, Fmn-binding Protein; Chain A

Domain ID domain_id	1ci0B00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Electron Transport, Fmn-binding Protein; Chain A

▶

8. Citations (1)

▶

Unit-cell length a length_a	74.970 Å
Unit-cell length b length_b	74.970 Å
Unit-cell length c length_c	157.140 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2300
R_work r_work	0.2250
R_free r_free	0.2740

fit	/app/data/saxs_computation/ci/1ci0/1ci0.fit
pddf	/app/data/pr_computation/ci/1ci0/1ci0.pr.out
profile	/app/data/saxs_computation/ci/1ci0/1ci0.dat

PNP OXIDASE FROM SACCHAROMYCES CEREVISIAE

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

PROTEIN (PNP OXIDASE)

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