SAXSdb — 7nms

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

Internalin B

Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

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 36–392	Mutation：T332E	SO4 SULFATE ION × 3 GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；Reservoir solution: 0.1 M succinate, pH 7.0, 0.2 M Li2SO4, 22.5 % PEG mixture consisting of equal amounts of eight low molecular weight PEGs (PEG 300, PEG 400, PEG 500MME, PEG 550MME, PEG 600, PEG 750MME, PEG 1,000, PEG 1,000MME); Protein solution: 10 mg/ml in 10 mM Tris, pH 8.0, 20 mM NaCl; Drop size: 100 nl + 100 nl (protein + reservoir)	Resolution 1.80 Å R-free 0.217

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 7NMS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7PV8 InlB392_T332E: T332E variant of Listeria monocytogenes InlB (internalin B) residues 36-392 Deposited 2021-10-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–392（357 aa）	Mutation：T332E	EDO 1,2-ETHANEDIOL × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Reservoir solution (Morpheus screen (Molecular Dimensions) condition G2): 0.1 M (imidazole / MES), pH 6.5; 20 % v/v ethylene glycol; 10 % w/v PEG 8,000; 0.02 M sodium formate; 0.02 M ammonium acetate; 0.02 M sodium citrate tribasic dehydrate; 0.02 M sodium potassium tartrate tetrahydrate; 0.02 M sodium oxamate; Protein solution: 10 mg/ml in 10 mM Tris, pH 8.0, 20 mM NaCl; Drop size: 100 nl + 100 nl (protein + reservoir)	Resolution 2.05 Å R-free 0.229
7PV9 Listeria monocytogene InlB (internalin B) residues 36-392 (internalin domain and B-repeat) Deposited 2021-10-01	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 36–392（357 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Reservoir solution (Morpheus screen (Molecular Dimensions) condition E6): 0.1 M (HEPES sodium salt / MOPS acid), pH 7.5, 20 % v/v ethylene glycol, 10 % w/v PEG 8,000, 0.03 M diethylene glycol, 0.03 M triethylene-glycol, 0.03 M tetraethylene glycol, 0.03 M pentaethylene glycol; Protein solution: 10 mg/ml in 10 mM Tris, pH 8.0, 20 mM NaCl; Drop size: 100 nl + 100 nl (protein + reservoir)	Resolution 3.30 Å R-free 0.272
7PV9 Listeria monocytogene InlB (internalin B) residues 36-392 (internalin domain and B-repeat) Deposited 2021-10-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 36–392（357 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Reservoir solution (Morpheus screen (Molecular Dimensions) condition E6): 0.1 M (HEPES sodium salt / MOPS acid), pH 7.5, 20 % v/v ethylene glycol, 10 % w/v PEG 8,000, 0.03 M diethylene glycol, 0.03 M triethylene-glycol, 0.03 M tetraethylene glycol, 0.03 M pentaethylene glycol; Protein solution: 10 mg/ml in 10 mM Tris, pH 8.0, 20 mM NaCl; Drop size: 100 nl + 100 nl (protein + reservoir)	Resolution 3.30 Å R-free 0.272
7PV9 Listeria monocytogene InlB (internalin B) residues 36-392 (internalin domain and B-repeat) Deposited 2021-10-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 36–392（357 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Reservoir solution (Morpheus screen (Molecular Dimensions) condition E6): 0.1 M (HEPES sodium salt / MOPS acid), pH 7.5, 20 % v/v ethylene glycol, 10 % w/v PEG 8,000, 0.03 M diethylene glycol, 0.03 M triethylene-glycol, 0.03 M tetraethylene glycol, 0.03 M pentaethylene glycol; Protein solution: 10 mg/ml in 10 mM Tris, pH 8.0, 20 mM NaCl; Drop size: 100 nl + 100 nl (protein + reservoir)	Resolution 3.30 Å R-free 0.272
8QP7 Crystal structure of Hepatitis C Virus E2 glycoprotein epitopeI 411-424 scaffold design 4CIL_04 Deposited 2023-09-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 84–321（238 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；25% (w/v) PEG 1500, 100 mM MMT buffer pH 9.0	Resolution 2.05 Å R-free 0.262
9QR4 InlB392_T336Y: T336Y variant of Listeria monocytogenes InlB (internalin B) residues 36-392 Deposited 2025-04-03	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 36–392（357 aa）	Mutation：T336Y	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Reservoir solution: MORPHEUS Screen, Condition F3: 0.1 M mixture of imidazole and MES (acid) pH 6.5, 10% PEG4000, 20% glycerol, 0.02 M of each monosaccaharide: D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine. Protein buffer: 10 mM Tris pH 8.0, 20 mM NaCl. Protein concentration: 10 mg/ml. Drop size: 1 ul protein + 1 ul reservoir.	Resolution 1.60 Å R-free 0.196
9QR4 InlB392_T336Y: T336Y variant of Listeria monocytogenes InlB (internalin B) residues 36-392 Deposited 2025-04-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 36–392（357 aa）	Mutation：T336Y	GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Reservoir solution: MORPHEUS Screen, Condition F3: 0.1 M mixture of imidazole and MES (acid) pH 6.5, 10% PEG4000, 20% glycerol, 0.02 M of each monosaccaharide: D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine. Protein buffer: 10 mM Tris pH 8.0, 20 mM NaCl. Protein concentration: 10 mg/ml. Drop size: 1 ul protein + 1 ul reservoir.	Resolution 1.60 Å R-free 0.196
9QR4 InlB392_T336Y: T336Y variant of Listeria monocytogenes InlB (internalin B) residues 36-392 Deposited 2025-04-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 36–392（357 aa）	Mutation：T336Y	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Reservoir solution: MORPHEUS Screen, Condition F3: 0.1 M mixture of imidazole and MES (acid) pH 6.5, 10% PEG4000, 20% glycerol, 0.02 M of each monosaccaharide: D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine. Protein buffer: 10 mM Tris pH 8.0, 20 mM NaCl. Protein concentration: 10 mg/ml. Drop size: 1 ul protein + 1 ul reservoir.	Resolution 1.60 Å R-free 0.196
9QR5 InlB392_V333E: V333E variant of Listeria monocytogenes InlB (internalin B) residues 36-392 Deposited 2025-04-03	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 36–392（357 aa）	Mutation：V333E	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；Reservoir solution: PEG Smear Screen Medium Molecular Weight, Condition E1: 0.1 M HEPES pH 7.5, 22.5% PEG medium molecular weight (MMW) mixture consisting of PEG1500, PEG2000, PEG2000MME, PEG3000, PEG3350, PEG4000, PEG5000MME. Protein Buffer: 10 mM Tris pH 8.0, 20 mM NaCl. Drop size: 200 nl protein + 100 nl reservoir.	Resolution 1.45 Å R-free 0.179

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

View Construct and Data Evidence

UniProt name	INLB_LISMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–362； UniProt 36–392

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	7nms
Deposition date deposition_date	2021-02-23
Structure title title	InlB392_T332E: T332E variant of Listeria monocytogenes InlB (internalin B) residues 36-392
Keywords keywords	LEUCINE RICH REPEAT, PROTEIN BINDING, PATHOGENICITY, VIRULENCE FACTOR, CELL INVASION; 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	30.83 Å
Radius of gyration Rg (electron density) rg_electron	30.86 Å
Forward intensity I(0) i0	25800000.00
Molecular weight molecular_weight	40566.0 kDa
Excluded volume excluded_volume	51218 Å³
Envelope volume envelope_volume	68364 Å³
Hydration-shell volume shell_volume	20471 Å³
Envelope diameter envelope_diameter	107.7 Å
Shell Rg shell_rg	33.97 Å
Envelope Rg envelope_rg	31.01 Å
Shape Rg shape_rg	30.90 Å
Total Rg total_rg	31.06 Å
Total atoms total_atoms	5743
Residues n_residues	357
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	99.9 Å
Rg (real space) rg_real	31.19 Å
Rg uncertainty (real space) rg_real_error	0.98 Å
I(0) (real space) i0_real	2.5800e+07
I(0) uncertainty (real space) i0_real_error	3.9980e+05
Rg (reciprocal space) rg_reciprocal	31.04 Å
I(0) (reciprocal space) i0_reciprocal	25800000.0000
Solution quality estimate total_estimate	0.5439
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.447
Kurtosis Kurtosis kurtosis	-0.615
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3579000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 0.997; Sysdev: 0.040; Positv: 1.000; Valcen: 0.428; Smooth: 0.314

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Internalin B
Molecular weight formula_weight	40449.8 kDa
Mutation mutation	T332E
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	6134

GPLGSETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKEVYTVSYDVDGEVIKTKVEAGTRITAPKPPTKQGYVFKGWYTEKNGGHEWNFNTDYMSGNDFTLYAVFKAET

来源 Source

来源生物 organism	Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
NCBI Class编号 ncbi_taxonomy_id	169963
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	329

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	7nmsA01
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	7nmsA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1220 —

Domain ID domain_id	7nmsA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	4270 — Listeria-Bacteroides repeat domain

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8. Citations (1)

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Unit-cell length a length_a	43.410 Å
Unit-cell length b length_b	88.730 Å
Unit-cell length c length_c	102.020 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	26.770 Å
R factor r_factor	0.1736
R_work r_work	0.1713
R_free r_free	0.2175

fit	/app/data/saxs_computation/nm/7nms/7nms.fit
pddf	/app/data/pr_computation/nm/7nms/7nms.pr.out
profile	/app/data/saxs_computation/nm/7nms/7nms.dat

InlB392_T332E: T332E variant of Listeria monocytogenes InlB (internalin B) residues 36-392

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

Internalin B

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