Yop effector YopM,Internalin B
Yersinia enterocolitica
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 84–321 | Not recorded | No other associated polymer | 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 |
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 8QP7 | 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 construct Different mutation/modification 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
36–392（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 construct Different mutation/modification 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
36–392（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 construct Different oligomeric state 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 construct Different oligomeric state 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 construct Different oligomeric state 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 |
| 9QR4 InlB392_T336Y: T336Y variant of Listeria monocytogenes InlB (internalin B) residues 36-392 Deposited 2025-04-03 | Different construct Different mutation/modification 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
36–392（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 construct Different mutation/modification 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
36–392（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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification 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
36–392（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 51–288； UniProt 84–321 |
