SAXSdb — 1o6t

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

INTERNALIN A

LISTERIA MONOCYTOGENES

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 36–496	Fragment：FUNCTIONAL DOMAIN, RESIDUES 36-496	MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 CL CHLORIDE ION × 4 SO4 SULFATE ION × 8 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；METHOD: VAPOUR DIFFUSION / HANGING DROP, PROTEIN: 10 MG/ML IN 10 MM HEPES PH 7.0, RESEVOIR: 10% PEG 4000, 100 MM MES/TRIS PH 6.0, 100 MM AMMONIUM SULFATE, 10 MM CACL2. CRYSTALS GREW APPROX 2 YEARS AFTER SETUP. TRUE CRYSTALLIZATION CONDITIONS PROBABLY DEVIATE FROM THOSE INDICATED	Resolution 1.60 Å R-free 0.161

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 1O6T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1O6S Internalin (Listeria monocytogenes) / E-Cadherin (human) Recognition Complex Deposited 2002-10-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–496（461 aa） Fragment：FUNCTIONAL DOMAIN, RESIDUES 36-496	Not recorded	CA CALCIUM ION × 2 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；VAPOUR DIFFUSION / HANGING DROP 10 MG/ML IN 10 MM HEPES PH 7.0, 26% PEG 4000, 100 MM MES/TRIS PH 7.0, 100 MM SODIUM ACETATE, 50 MM CACL2	Resolution 1.80 Å R-free 0.221
1O6V Internalin (INLA, Listeria monocytogenes) - functional domain, uncomplexed Deposited 2002-10-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–496（461 aa） Fragment：FUNCTIONAL DOMAIN, RESIDUES 36-496	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；METHOD: VAPOUR DIFFUSION / HANGING DROP PROTEIN: 10 MG/ML IN 10 MM HEPES PH 7.0 RESEVOIR: 10% PEG 4000, 100 MM MES/TRIS PH 6.0, 100 MM AMMONIUM SULFATE, 10 MM CACL2	Resolution 1.50 Å R-free 0.184
1O6V Internalin (INLA, Listeria monocytogenes) - functional domain, uncomplexed Deposited 2002-10-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 36–496（461 aa） Fragment：FUNCTIONAL DOMAIN, RESIDUES 36-496	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；METHOD: VAPOUR DIFFUSION / HANGING DROP PROTEIN: 10 MG/ML IN 10 MM HEPES PH 7.0 RESEVOIR: 10% PEG 4000, 100 MM MES/TRIS PH 6.0, 100 MM AMMONIUM SULFATE, 10 MM CACL2	Resolution 1.50 Å R-free 0.184
2OMT Crystal structure of InlA G194S+S/hEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–497（462 aa） Fragment：internalin domain	Mutation：G194S+S	CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K	Resolution 2.00 Å R-free 0.283
2OMU Crystal structure of InlA G194S+S Y369S/hEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–497（462 aa） Fragment：internalin domain	Mutation：G194S+S Y369S	CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K	Resolution 1.80 Å R-free 0.217
2OMV Crystal structure of InlA S192N Y369S/hEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–495（460 aa） Fragment：internalin domain	Mutation：S192N Y369S	CA CALCIUM ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K	Resolution 1.90 Å R-free 0.219
2OMW Crystal structure of InlA S192N Y369S/mEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–496（461 aa） Fragment：internalin domain	Mutation：S192N Y369S	CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；PEG 6000, LiCl, Na-Citrate, pH 5.2, vapor diffusion, hanging drop, temperature 298K	Resolution 1.85 Å R-free 0.207
2OMX Crystal structure of InlA S192N G194S+S/hEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–497（462 aa） Fragment：internalin domain	Mutation：S192N G194S+S	CL CHLORIDE ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K	Resolution 1.70 Å R-free 0.223
2OMY Crystal structure of InlA S192N/hEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–495（460 aa） Fragment：internalin domain	Mutation：S192N	CA CALCIUM ION × 2 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K	Resolution 1.70 Å R-free 0.211
2OMZ Crystal structure of InlA Y369A/hEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–495（460 aa） Fragment：internalin domain	Mutation：Y369A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K	Resolution 1.60 Å R-free 0.186

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	INLA_LISMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–466； UniProt 36–496

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	1o6t
Deposition date deposition_date	2002-10-15
Structure title title	Internalin (INLA, Listeria monocytogenes) - functional domain, uncomplexed
Keywords keywords	CELL INVASION, BACTERIAL INFECTION, LEUCINE RICH REPEAT, CELL ADHESION, CELL-WALL SURFACE PROTEIN; CELL INVASION
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	30.77 Å
Radius of gyration Rg (electron density) rg_electron	30.61 Å
Forward intensity I(0) i0	41617300.00
Molecular weight molecular_weight	50945.0 kDa
Excluded volume excluded_volume	63773 Å³
Envelope volume envelope_volume	80765 Å³
Hydration-shell volume shell_volume	23034 Å³
Envelope diameter envelope_diameter	111.0 Å
Shell Rg shell_rg	35.94 Å
Envelope Rg envelope_rg	30.53 Å
Shape Rg shape_rg	30.64 Å
Total Rg total_rg	30.94 Å
Total atoms total_atoms	3568
Residues n_residues	462
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	104.6 Å
Rg (real space) rg_real	31.04 Å
Rg uncertainty (real space) rg_real_error	1.12 Å
I(0) (real space) i0_real	4.1620e+07
I(0) uncertainty (real space) i0_real_error	7.3140e+05
Rg (reciprocal space) rg_reciprocal	30.93 Å
I(0) (reciprocal space) i0_reciprocal	41610000.0000
Solution quality estimate total_estimate	0.8077
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.6 Å
Skewness Skewness skewness	0.441
Kurtosis Kurtosis kurtosis	-0.472
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9970000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.744; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.532; Smooth: 0.735

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	INTERNALIN A
Molecular weight formula_weight	50239.1 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	5098

GPLGSATITQDTPINQIFTDTALAEKMKTVLGKTNVTDTVSQTDLDQVTTLQADRLGIKSIDGVEYLNNLTQINFSNNQLTDITPLKNLTKLVDILMNNNQIADITPLANLTNLTGLTLFNNQITDIDPLKNLTNLNRLELSSNTISDISALSGLTSLQQLSFGNQVTDLKPLANLTTLERLDISSNKVSDISVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIGTLASLTNLTDLDLANNQISNLAPLSGLTKLTELKLGANQISNISPLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNISDISPVSSLTKLQRLFFYNNKVSDVSSLANLTNINWLSAGHNQISDLTPLANLTRITQLGLNDQAWTNAPVNYKANVSIPNTVKNVTGALIAPATISDGGSYTEPDITWNLPSYTNEVSYTFSQPVTIGKGTTTFSGTVTQPLKA

来源 Source

来源生物 organism	LISTERIA MONOCYTOGENES
NCBI Class编号 ncbi_taxonomy_id	169963
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	702

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1o6ta1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.15 — Internalin Ig-like domain

Domain ID domain_id	d1o6ta2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamily	c.10.2 — L domain-like
Family Family family	c.10.2.1 — Internalin LRR domain

Domain ID domain_id	d1o6ta3
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 (2 domains)

Domain ID domain_id	1o6tA01
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	1o6tA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1220 —

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8. Citations (1)

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Unit-cell length a length_a	95.919 Å
Unit-cell length b length_b	55.881 Å
Unit-cell length c length_c	97.780 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.07 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	91.290 Å
R factor r_factor	0.1330
R_work r_work	0.1310
R_free r_free	0.1610

fit	/app/data/saxs_computation/o6/1o6t/1o6t.fit
pddf	/app/data/pr_computation/o6/1o6t/1o6t.pr.out
profile	/app/data/saxs_computation/o6/1o6t/1o6t.dat

Internalin (INLA, Listeria monocytogenes) - functional domain, uncomplexed