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9qr4

InlB392_T336Y: T336Y variant of Listeria monocytogenes InlB (internalin B) residues 36-392

Method: X-RAY DIFFRACTION Dmax: 172.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Internalin B

Listeria monocytogenes EGD-e

UniProt P0DQD2

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：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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 36–392 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 36–392 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

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 9QR4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7NMS InlB392_T332E: T332E variant of Listeria monocytogenes InlB (internalin B) residues 36-392 Deposited 2021-02-23 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：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
7PV8 InlB392_T332E: T332E variant of Listeria monocytogenes InlB (internalin B) residues 36-392 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）
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
9QR5 InlB392_V333E: V333E variant of Listeria monocytogenes InlB (internalin B) residues 36-392 Deposited 2025-04-03 Different mutation/modification 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 7 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 Author chain B； PDBConstruct 6–362； UniProt 36–392 Author chain C； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 9qr4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9qr4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9qr4
Deposition date deposition_date2025-04-03
Structure title titleInlB392_T336Y: T336Y variant of Listeria monocytogenes InlB (internalin B) residues 36-392
Keywords keywordsLEUCINE RICH REPEAT, PROTEIN BINDING, PATHOGENICITY, VIRULENCE FACTOR, CELL INVASION; CELL INVASION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier46.17 Å
Radius of gyration Rg (electron density) rg_electron46.71 Å
Forward intensity I(0) i0205752000.00
Molecular weight molecular_weight121060.0 kDa
Excluded volume excluded_volume153520 ų
Envelope volume envelope_volume231100 ų
Hydration-shell volume shell_volume46003 ų
Envelope diameter envelope_diameter166.6 Å
Shell Rg shell_rg43.81 Å
Envelope Rg envelope_rg47.37 Å
Shape Rg shape_rg46.82 Å
Total Rg total_rg46.15 Å
Total atoms total_atoms17229
Residues n_residues1072
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax172.7 Å
Rg (real space) rg_real46.76 Å
Rg uncertainty (real space) rg_real_error2.55 Å
I(0) (real space) i0_real2.0580e+08
I(0) uncertainty (real space) i0_real_error4.3410e+06
Rg (reciprocal space) rg_reciprocal46.18 Å
I(0) (reciprocal space) i0_reciprocal205600000.0000
Solution quality estimate total_estimate0.7460
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary55.9 Å
Skewness Skewness skewness0.598
Kurtosis Kurtosis kurtosis-0.035
Angular range angular_range— – 0.1700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9234000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.620; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.834; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)