SAXSdb — 4ps6

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

Inhibitor of vertebrate lysozyme

Pseudomonas aeruginosa

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 25–153	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.2M ammonium acetate, 30.0% polyethylene glycol 4000, 0.1M sodium acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.25 Å R-free 0.164

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 4PS6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1UUZ IVY:A NEW FAMILY OF PROTEIN Deposited 2004-01-12	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 25–153（129 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% POLYETHYLENEGLYCOL 4000, IMIDAZOLE/MALATE 0.2M PH 6.0, 5% GLYCEROL	Resolution 1.80 Å R-free 0.250
1UUZ IVY:A NEW FAMILY OF PROTEIN Deposited 2004-01-12	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 25–153（129 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% POLYETHYLENEGLYCOL 4000, IMIDAZOLE/MALATE 0.2M PH 6.0, 5% GLYCEROL	Resolution 1.80 Å R-free 0.250

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

View Construct and Data Evidence

UniProt name	IVY_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–130； UniProt 25–153

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	4ps6
Deposition date deposition_date	2014-03-06
Structure title title	Crystal structure of an inhibitor of vertebrate lysozyme (PA3902) from Pseudomonas aeruginosa PAO1 at 1.25 A resolution
Keywords keywords	;PF08816 family, Ivy, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, TOXIN ;; TOXIN
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	15.63 Å
Radius of gyration Rg (electron density) rg_electron	14.38 Å
Forward intensity I(0) i0	4544190.00
Molecular weight molecular_weight	14661.0 kDa
Excluded volume excluded_volume	18056 Å³
Envelope volume envelope_volume	20594 Å³
Hydration-shell volume shell_volume	12315 Å³
Envelope diameter envelope_diameter	49.8 Å
Shell Rg shell_rg	19.95 Å
Envelope Rg envelope_rg	14.72 Å
Shape Rg shape_rg	14.36 Å
Total Rg total_rg	15.50 Å
Total atoms total_atoms	1023
Residues n_residues	127
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	51.2 Å
Rg (real space) rg_real	15.54 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	4.5440e+06
I(0) uncertainty (real space) i0_real_error	5.5940e+04
Rg (reciprocal space) rg_reciprocal	15.55 Å
I(0) (reciprocal space) i0_reciprocal	4544000.0000
Solution quality estimate total_estimate	0.8815
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.4 Å
Skewness Skewness skewness	0.185
Kurtosis Kurtosis kurtosis	-0.318
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	973300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.992

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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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4ps6a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.233 — Inhibitor of vertebrate lysozyme, Ivy
Superfamily Superfamily superfamily	d.233.1 — Inhibitor of vertebrate lysozyme, Ivy
Family Family family	d.233.1.1 — Inhibitor of vertebrate lysozyme, Ivy

Domain ID domain_id	d4ps6a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	4ps6A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1420 — Inhibitor of vertebrate lysozyme, Ivy
Homologous superfamily homologous superfamily	10 — Inhibitor of vertebrate lysozyme

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8. Citations (1)

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Unit-cell length a length_a	33.449 Å
Unit-cell length b length_b	47.057 Å
Unit-cell length c length_c	36.389 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.91 °
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	1.250 Å
Low-resolution limit resolution_low	36.126 Å
R factor r_factor	0.1185
R_work r_work	0.1161
R_free r_free	0.1639

Description description	Inhibitor of vertebrate lysozyme
Molecular weight formula_weight	14675.9 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	1352

Crystal structure of an inhibitor of vertebrate lysozyme (PA3902) from Pseudomonas aeruginosa PAO1 at 1.25 A resolution

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

Inhibitor of vertebrate lysozyme

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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Pseudomonas aeruginosa
NCBI Class编号 ncbi_taxonomy_id	208964
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	300

fit	/app/data/saxs_computation/ps/4ps6/4ps6.fit
pddf	/app/data/pr_computation/ps/4ps6/4ps6.pr.out
profile	/app/data/saxs_computation/ps/4ps6/4ps6.dat