SAXSdb — 1cwv

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

INVASIN

Yersinia pseudotuberculosis

UniProt P11922

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 495–986	Fragment：C-TERMINAL EXTRACELLULAR FRAGMENT	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；PEG 4000, SODIUM CITRATE, ISOPROPANOL, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.30 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.

Other PDB	Difference from Current Entry 1CWV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4E1T X-ray crystal structure of the transmembrane beta-domain from invasin from Yersinia pseudotuberculosis Deposited 2012-03-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 147–390（244 aa） Fragment：transmembrane domain (UNP residues 147-390)	Mutation：L352F	OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 12 OLB (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE MONOOLEIN；pH 4；294 K；0.05 M sodium citrate, pH 3.8-4.4, 0.2 M lithium sulfate, 23-35% PEG400, LIPIDIC CUBIC PHASE MONOOLEIN, temperature 294K	Resolution 2.26 Å R-free 0.260

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

View Construct and Data Evidence

UniProt name	INVA_YERPS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–492； UniProt 495–986

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	1cwv
Deposition date deposition_date	1999-08-26
Structure title title	CRYSTAL STRUCTURE OF INVASIN: A BACTERIAL INTEGRIN-BINDING PROTEIN
Keywords keywords	INTEGRIN-BINDING PROTEIN, INV GENE, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	53.30 Å
Radius of gyration Rg (electron density) rg_electron	54.91 Å
Forward intensity I(0) i0	40393400.00
Molecular weight molecular_weight	51215.0 kDa
Excluded volume excluded_volume	63855 Å³
Envelope volume envelope_volume	92942 Å³
Hydration-shell volume shell_volume	18614 Å³
Envelope diameter envelope_diameter	190.6 Å
Shell Rg shell_rg	39.42 Å
Envelope Rg envelope_rg	55.01 Å
Shape Rg shape_rg	54.92 Å
Total Rg total_rg	54.16 Å
Total atoms total_atoms	3606
Residues n_residues	484
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	178.6 Å
Rg (real space) rg_real	54.50 Å
Rg uncertainty (real space) rg_real_error	2.97 Å
I(0) (real space) i0_real	4.0390e+07
I(0) uncertainty (real space) i0_real_error	9.0530e+05
Rg (reciprocal space) rg_reciprocal	52.27 Å
I(0) (reciprocal space) i0_reciprocal	40270000.0000
Solution quality estimate total_estimate	0.5469
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.572
Kurtosis Kurtosis kurtosis	-0.683
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	981400.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.029; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.019; Smooth: 0.002

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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	INVASIN
Molecular weight formula_weight	51939.4 kDa
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	3801

SVTVQQPQLTLTAAVIGDGAPANGKTAITVEFTVADFEGKPLAGQEVVITTNNGALPNKITEKTDANGVARIALTNTTDGVTVVTAEVEGQRQSVDTHFVKGTIAADKSTLAAVPTSIIADGLMASTITLELKDTYGDPQAGANVAFDTTLGNMGVITDHNDGTYSAPLTSTTLGVATVTVKVDGAAFSVPSVTVNFTADPIPDAGRSSFTVSTPDILADGTMSSTLSFVPVDKNGHFISGMQGLSFTQNGVPVSISPITEQPDSYTATVVGNSVGDVTITPQVDTLILSTLQKKISLFPVPTLTGILVNGQNFATDKGFPKTIFKNATFQLQMDNDVANNTQYEWSSSFTPNVSVNDQGQVTITYQTYSEVAVTAKSKKFPSYSVSYRFYPNRWIYDGGRSLVSSLEASRQCQGSDMSAVLESSRATNGTRAPDGTLWGEWGSLTAYSSDWQSGEYWVKKTSTDFETMNMDTGALQPGPAYLAFPLCALSI

来源 Source

来源生物 organism	Yersinia pseudotuberculosis
NCBI Class编号 ncbi_taxonomy_id	633
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
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	195

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1cwva1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.14 — Invasin/intimin cell-adhesion fragments
Family Family family	b.1.14.1 — Invasin/intimin cell-adhesion fragments

Domain ID domain_id	d1cwva2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.14 — Invasin/intimin cell-adhesion fragments
Family Family family	b.1.14.1 — Invasin/intimin cell-adhesion fragments

Domain ID domain_id	d1cwva3
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.14 — Invasin/intimin cell-adhesion fragments
Family Family family	b.1.14.1 — Invasin/intimin cell-adhesion fragments

Domain ID domain_id	d1cwva4
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.14 — Invasin/intimin cell-adhesion fragments
Family Family family	b.1.14.1 — Invasin/intimin cell-adhesion fragments

Domain ID domain_id	d1cwva5
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.3 — Invasin/intimin cell-adhesion fragment, C-terminal domain

CATH v4.4 (5 domains)

Domain ID domain_id	1cwvA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1cwvA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1cwvA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1cwvA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1080 —

Domain ID domain_id	1cwvA05
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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8. Citations (1)

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Unit-cell length a length_a	61.140 Å
Unit-cell length b length_b	50.660 Å
Unit-cell length c length_c	97.920 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.34 °
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	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2740

fit	/app/data/saxs_computation/cw/1cwv/1cwv.fit
pddf	/app/data/pr_computation/cw/1cwv/1cwv.pr.out
profile	/app/data/saxs_computation/cw/1cwv/1cwv.dat

CRYSTAL STRUCTURE OF INVASIN: A BACTERIAL INTEGRIN-BINDING PROTEIN

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

INVASIN

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