SAXSdb — 8h63

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

Internalin A

Listeria monocytogenes serovar 1/2a

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 36–496	Not recorded	VHH10 × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 IPA ISOPROPYL ALCOHOL × 1 GOL GLYCEROL × 2 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.15 K；0.085 M HEPES sodium pH 7.0; 8.5% Isopropanol; 20% PEG 4,000	Resolution 1.53 Å R-free 0.190

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 8H63	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8H62 Crystal structure of Internalin A from Listeria monocytogenes with human E-cadherin EC12 Deposited 2022-10-14	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）	Not recorded	CA CALCIUM ION × 4 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium acetate 45% MPD	Resolution 1.91 Å R-free 0.210
8H64 Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH24 bound Deposited 2022-10-15	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）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Amonium citrate tribasic pH 7.0; 14% PEG 4,000	Resolution 2.35 Å R-free 0.227
8H64 Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH24 bound Deposited 2022-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 36–496（461 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Amonium citrate tribasic pH 7.0; 14% PEG 4,000	Resolution 2.35 Å R-free 0.227
8H64 Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH24 bound Deposited 2022-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 36–496（461 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Amonium citrate tribasic pH 7.0; 14% PEG 4,000	Resolution 2.35 Å R-free 0.227
8H64 Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH24 bound Deposited 2022-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 36–496（461 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Amonium citrate tribasic pH 7.0; 14% PEG 4,000	Resolution 2.35 Å R-free 0.227

2 other PDB entries and 5 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 2–462； 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	8h63
Deposition date deposition_date	2022-10-15
Structure title title	Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH10 bound
Keywords keywords	;Internalin A Cadherin Bacterial invasion nanobody Surface plasmon resonance Isothermal titration calorimetry, CELL INVASION, CELL INVASION-IMMUNE SYSTEM complex ;; CELL INVASION/IMMUNE SYSTEM
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	29.03 Å
Radius of gyration Rg (electron density) rg_electron	28.70 Å
Forward intensity I(0) i0	63119000.00
Molecular weight molecular_weight	62765.0 kDa
Excluded volume excluded_volume	78748 Å³
Envelope volume envelope_volume	96552 Å³
Hydration-shell volume shell_volume	29264 Å³
Envelope diameter envelope_diameter	107.2 Å
Shell Rg shell_rg	34.38 Å
Envelope Rg envelope_rg	28.77 Å
Shape Rg shape_rg	28.69 Å
Total Rg total_rg	29.25 Å
Total atoms total_atoms	4410
Residues n_residues	581
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	102.3 Å
Rg (real space) rg_real	29.15 Å
Rg uncertainty (real space) rg_real_error	1.00 Å
I(0) (real space) i0_real	6.3120e+07
I(0) uncertainty (real space) i0_real_error	9.7020e+05
Rg (reciprocal space) rg_reciprocal	29.10 Å
I(0) (reciprocal space) i0_reciprocal	63120000.0000
Solution quality estimate total_estimate	0.8482
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.5 Å
Skewness Skewness skewness	0.482
Kurtosis Kurtosis kurtosis	-0.105
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14530000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.811; Smooth: 0.883

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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	49914.8 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	5311

SATITQDTPINQIFTDTALAEKMKTVLGKTNVTDTVSQTDLDQVTTLQADRLGIKSIDGVEYLNNLTQINFSNNQLTDITPLKNLTKLVDILMNNNQIADITPLANLTNLTGLTLFNNQITDIDPLKNLTNLNRLELSSNTISDISALSGLTSLQQLSFGNQVTDLKPLANLTTLERLDISSNKVSDISVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIGTLASLTNLTDLDLANNQISNLAPLSGLTKLTELKLGANQISNISPLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNISDISPVSSLTKLQRLFFYNNKVSDVSSLANLTNINWLSAGHNQISDLTPLANLTRITQLGLNDQAWTNAPVNYKANVSIPNTVKNVTGALIAPATISDGGSYTEPDITWNLPSYTNEVSYTFSQPVTIGKGTTTFSGTVTQPLKA

来源 Source

来源生物 organism	Listeria monocytogenes serovar 1/2a
NCBI Class编号 ncbi_taxonomy_id	169963
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	VHH10
Molecular weight formula_weight	12732.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ELQLVESGGGLVQAGGSLTVSCAASGSAFSVNVMGWSRQAPGKERELVAGITRRGNTYYADTVKGRFTISRDNAKNTLYLQMNSLKPEDTAMYYCAALADIATMGPNDYWGQGTQVTVSG

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli BL21

Entity 3 Entity 3 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	763

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8. Citations (1)

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Unit-cell length a length_a	151.581 Å
Unit-cell length b length_b	52.420 Å
Unit-cell length c length_c	103.060 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	128.65 °
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	1.530 Å
Low-resolution limit resolution_low	31.550 Å
R factor r_factor	0.1617
R_work r_work	0.1610
R_free r_free	0.1902

fit	/app/data/saxs_computation/h6/8h63/8h63.fit
pddf	/app/data/pr_computation/h6/8h63/8h63.pr.out
profile	/app/data/saxs_computation/h6/8h63/8h63.dat

Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH10 bound

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

Internalin A

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)