4cil

YopM-InlB: Hybrid leucine-rich repeat protein

Method: X-RAY DIFFRACTION D_max: 83.5 Å Quality: GOOD

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

YOPM-CAP, INTERNALIN B

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	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 93–321	Fragment：YOPM N-TERMINAL CAP RESIDUES 34-87, INLB LEUCINE-RICH REPEAT AND INTER-REPEAT REGION RESIDUES 93-321	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；HANGING DROP VAPOUR DIFFUSION AT 293 K WITH A DROP SIZE OF 2 UL CONSISTING OF EQUAL VOLUMES OF PROTEIN AT A CONCENTRATION OF 10 MG/ML AND RESERVOIR SOLUTION (0.1 M TRICINE, PH 9.0, 28% PEG 1000, 10% GLYCEROL, 0.25M KCL). CRYSTALS WERE CRYO-PROTECTED WITH RESERVOIR-SOLUTION ADDITIONALLY CONTAINING 15% GLYCEROL AND FLASH-FROZEN IN LIQUID NITROGEN	Resolution 1.50 Å R-free 0.219

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 4CIL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D0B INTERNALIN B LEUCINE RICH REPEAT DOMAIN Deposited 1999-09-09	Different construct 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 36–248（213 aa） Fragment：LRR DOMAIN, RESIDUES 36-248	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM MES, 200 mM Calcium Acetate, 20% PEG 8000, 1 mM DTT , pH 6.5, vapor diffusion, temperature 298K	Resolution 1.86 Å R-free 0.235
1H6T Internalin B: crystal structure of fused N-terminal domains. Deposited 2001-06-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–321（286 aa） Fragment：LRR DOMAIN, RESIDUES 36-321	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；293 K；0.2M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 5.0, 13% W/V PEG 4000, 6% V/V 2-METHYL-2,4-PENTANDIOL, T=20C, PROTEIN CONC.=10 MG/ML	Resolution 1.60 Å R-free 0.197
1M9S Crystal structure of Internalin B (InlB), a Listeria monocytogenes virulence protein containing SH3-like domains. Deposited 2002-07-29	Different construct 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 36–630（595 aa）	Not recorded	TB TERBIUM(III) ION × 7 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；lithium sulfate, glycerol, dithiothreitol, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.65 Å R-free 0.302
1OTM Calcium-binding mutant of the internalin B LRR domain Deposited 2003-03-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–248（213 aa） Fragment：LRR domain	Mutation：D51A, D59A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Peg 8000, Mes, Calcium acetate, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.93 Å R-free 0.240
1OTN Calcium-binding mutant of the Internalin B LRR domain Deposited 2003-03-21	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 36–248（213 aa） Fragment：LRR domain	Mutation：D51A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Peg 8000, Mes, Calcium acetate, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.97 Å R-free 0.244
1OTO Calcium-binding mutant of the internalin B LRR domain Deposited 2003-03-21	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 36–248（213 aa） Fragment：LRR domain	Mutation：D59A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Peg 8000, Mes, Calcium acetate, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.96 Å R-free 0.230
2UZX Structure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein InlB: Crystal form I Deposited 2007-05-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–321（286 aa） Fragment：INTERNALIN DOMAIN (CAP, LRR, IR), INLB321, RESIDUES 36-320	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 DEG C VAPOR DIFFUSION. 2 UL PROTEIN (5 MG/ML) PLUS 1 UL RESERVOIR CONSISTING OF 16.5% PEG 1500, 4.4% MPD, 0.1 M TRIS, PH8.5. RESERVOIR WAS COVERED WITH ALS OIL.	Resolution 2.80 Å R-free 0.307
2UZX Structure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein InlB: Crystal form I Deposited 2007-05-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 36–321（286 aa） Fragment：INTERNALIN DOMAIN (CAP, LRR, IR), INLB321, RESIDUES 36-320	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 DEG C VAPOR DIFFUSION. 2 UL PROTEIN (5 MG/ML) PLUS 1 UL RESERVOIR CONSISTING OF 16.5% PEG 1500, 4.4% MPD, 0.1 M TRIS, PH8.5. RESERVOIR WAS COVERED WITH ALS OIL.	Resolution 2.80 Å R-free 0.307
2UZY Structure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein inlb: low resolution, Crystal form II Deposited 2007-05-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–321（286 aa） Fragment：INTERNALIN DOMAIN (CAP, LRR, IR)\: INLB321, RESIDUES 36-321	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；VAPOR DIFFUSION AT 25 DEGREE C IN SITTING-DROPS. 2 UL PROTEIN (8 MG/ML)PLUS 2 UL RESERVOIR (1.4 M NA/K PHOSPHATE, PH 6.5, 10% PEG 2000 MONO-METHYL-ETHER)	Resolution 4.00 Å R-free 0.301
2UZY Structure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein inlb: low resolution, Crystal form II Deposited 2007-05-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 36–321（286 aa） Fragment：INTERNALIN DOMAIN (CAP, LRR, IR)\: INLB321, RESIDUES 36-321	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；VAPOR DIFFUSION AT 25 DEGREE C IN SITTING-DROPS. 2 UL PROTEIN (8 MG/ML)PLUS 2 UL RESERVOIR (1.4 M NA/K PHOSPHATE, PH 6.5, 10% PEG 2000 MONO-METHYL-ETHER)	Resolution 4.00 Å R-free 0.301
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form Deposited 2009-08-27	Different construct 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 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS.	Resolution 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form Deposited 2009-08-27	Different construct 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 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS.	Resolution 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form Deposited 2009-08-27	Different construct 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 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS.	Resolution 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form Deposited 2009-08-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS.	Resolution 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form Deposited 2009-08-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS.	Resolution 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form Deposited 2009-08-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS.	Resolution 2.60 Å R-free 0.249
2WQV Internalin domain of Listeria monocytogenes InlB: rhombohedral crystal form Deposited 2009-08-27	Different construct 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 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；SITTING VAPOR DIFFUSION AT 293 K. 200 NL PROTEIN PLUS 100 NL OF RESERVOIR SOLUTION CONSISTING OF 0.1 M NACL, 0.1 M CHES PH 9.5, 40% PEG300. THE PROTEIN WAS ACTUALLY A COMPLEX OF MET741 WITH INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG/ML. CRYSTAL GROWTH TIME: SEVERAL WEEKS TO MONTHS.	Resolution 2.80 Å R-free 0.238
2WQV Internalin domain of Listeria monocytogenes InlB: rhombohedral crystal form Deposited 2009-08-27	Different construct 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 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；SITTING VAPOR DIFFUSION AT 293 K. 200 NL PROTEIN PLUS 100 NL OF RESERVOIR SOLUTION CONSISTING OF 0.1 M NACL, 0.1 M CHES PH 9.5, 40% PEG300. THE PROTEIN WAS ACTUALLY A COMPLEX OF MET741 WITH INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG/ML. CRYSTAL GROWTH TIME: SEVERAL WEEKS TO MONTHS.	Resolution 2.80 Å R-free 0.238
2WQW DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER of the Listeria monocytogenes InlB internalin domain Deposited 2009-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Mutation：YES	PEG DI(HYDROXYETHYL)ETHER × 12	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.5；293 K；293 K. PROTEIN (6.7 MG/ML) PLUS RESERVOIR = 2 PLUS 1. RESERVOIR SOLUTION IS 44-52% PEG2000, 0.1 M CHES PH=9,5, 0.2M NACL., PH 9.5	Resolution 2.24 Å R-free 0.239
2WQW DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER of the Listeria monocytogenes InlB internalin domain Deposited 2009-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Mutation：YES	PEG DI(HYDROXYETHYL)ETHER × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.5；293 K；293 K. PROTEIN (6.7 MG/ML) PLUS RESERVOIR = 2 PLUS 1. RESERVOIR SOLUTION IS 44-52% PEG2000, 0.1 M CHES PH=9,5, 0.2M NACL., PH 9.5	Resolution 2.24 Å R-free 0.239
2WQX InlB321_4R: S199R, D200R, G206R, A227R, C242A mutant of the Listeria monocytogenes InlB internalin domain Deposited 2009-08-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP VAPOUR DIFFUSION AT 293K WITH 1 UL PROTEIN (3.8 MG/ML IN 50 MM HEPES, PH 7.0, 100 MM NACL) PLUS 0.5 UL RESERVOIR (17% PEG1000MME, 90 MM NA-CITRATE).	Resolution 2.03 Å R-free 0.257
2WQX InlB321_4R: S199R, D200R, G206R, A227R, C242A mutant of the Listeria monocytogenes InlB internalin domain Deposited 2009-08-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP VAPOUR DIFFUSION AT 293K WITH 1 UL PROTEIN (3.8 MG/ML IN 50 MM HEPES, PH 7.0, 100 MM NACL) PLUS 0.5 UL RESERVOIR (17% PEG1000MME, 90 MM NA-CITRATE).	Resolution 2.03 Å R-free 0.257
2Y5P B-repeat of Listeria monocytogenes InlB (internalin B) Deposited 2011-01-17	Different construct 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 322–392（71 aa） Fragment：B-REPEAT, RESIDUES 322-392	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 DEG C IN HANGING OR SITTING-DROPS WITH 2 UL PROTEIN (17.3 MG/ML) PLUS 1 UL RESERVOIR (0.1 M NA-ACETATE PH 5.0, 0.2 M CACL2, 18 % PEG 6000).	Resolution 1.30 Å R-free 0.196
2Y5P B-repeat of Listeria monocytogenes InlB (internalin B) Deposited 2011-01-17	Different construct 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 322–392（71 aa） Fragment：B-REPEAT, RESIDUES 322-392	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 DEG C IN HANGING OR SITTING-DROPS WITH 2 UL PROTEIN (17.3 MG/ML) PLUS 1 UL RESERVOIR (0.1 M NA-ACETATE PH 5.0, 0.2 M CACL2, 18 % PEG 6000).	Resolution 1.30 Å R-free 0.196
2Y5P B-repeat of Listeria monocytogenes InlB (internalin B) Deposited 2011-01-17	Different construct 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 322–392（71 aa） Fragment：B-REPEAT, RESIDUES 322-392	Not recorded	CA CALCIUM ION × 3 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 DEG C IN HANGING OR SITTING-DROPS WITH 2 UL PROTEIN (17.3 MG/ML) PLUS 1 UL RESERVOIR (0.1 M NA-ACETATE PH 5.0, 0.2 M CACL2, 18 % PEG 6000).	Resolution 1.30 Å R-free 0.196
2Y5P B-repeat of Listeria monocytogenes InlB (internalin B) Deposited 2011-01-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 322–392（71 aa） Fragment：B-REPEAT, RESIDUES 322-392	Not recorded	CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 DEG C IN HANGING OR SITTING-DROPS WITH 2 UL PROTEIN (17.3 MG/ML) PLUS 1 UL RESERVOIR (0.1 M NA-ACETATE PH 5.0, 0.2 M CACL2, 18 % PEG 6000).	Resolution 1.30 Å R-free 0.196
2Y5P B-repeat of Listeria monocytogenes InlB (internalin B) Deposited 2011-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 322–392（71 aa） Fragment：B-REPEAT, RESIDUES 322-392 Chain B 322–392（71 aa） Fragment：B-REPEAT, RESIDUES 322-392 Chain C 322–392（71 aa） Fragment：B-REPEAT, RESIDUES 322-392 Chain D 322–392（71 aa） Fragment：B-REPEAT, RESIDUES 322-392	Not recorded	CA CALCIUM ION × 8 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 DEG C IN HANGING OR SITTING-DROPS WITH 2 UL PROTEIN (17.3 MG/ML) PLUS 1 UL RESERVOIR (0.1 M NA-ACETATE PH 5.0, 0.2 M CACL2, 18 % PEG 6000).	Resolution 1.30 Å R-free 0.196
2Y5Q Listeria monocytogenes InlB (internalin B) residues 36-392 Deposited 2011-01-17	Different construct 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） Fragment：INTERNALIN DOMAIN AND B-REPEAT, RESIDUES 36-392	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 DEG C IN HANGING OR SITTING-DROPS WITH 1.5 UL PROTEIN (5 MG/ML) PLUS 1.5 UL RESERVOIR (0.1 M MES, PH 5.5, 14 % MPD) MICROSEEDED FROM A SIMILAR CONDITION (0.1 M MES PH 6.0, 6.5 % PEG6000 AND 5 MM ZNCL2).	Resolution 3.20 Å R-free 0.225
2Y5Q Listeria monocytogenes InlB (internalin B) residues 36-392 Deposited 2011-01-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 36–392（357 aa） Fragment：INTERNALIN DOMAIN AND B-REPEAT, RESIDUES 36-392	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 DEG C IN HANGING OR SITTING-DROPS WITH 1.5 UL PROTEIN (5 MG/ML) PLUS 1.5 UL RESERVOIR (0.1 M MES, PH 5.5, 14 % MPD) MICROSEEDED FROM A SIMILAR CONDITION (0.1 M MES PH 6.0, 6.5 % PEG6000 AND 5 MM ZNCL2).	Resolution 3.20 Å R-free 0.225
4AW4 Engineered variant of Listeria monocytogenes InlB internalin domain with an additional leucine rich repeat inserted Deposited 2012-05-31	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 36–98（63 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321 Chain A 99–321（223 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Not recorded	SO4 SULFATE ION × 9 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP VAPOUR DIFFUSION IN 96-WELL PLATES AT 20 DEGREE C. 17 MG/ML PROTEIN IN 25 MM TRIS, PH 8, 20 MM NACL. RESERVOIR SOLUTION WAS 2M AMMONIUM SULFATE. DROPS WERE SET UP WITH EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION.	Resolution 1.93 Å R-free 0.205
4AW4 Engineered variant of Listeria monocytogenes InlB internalin domain with an additional leucine rich repeat inserted Deposited 2012-05-31	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 36–98（63 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321 Chain B 99–321（223 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Not recorded	SO4 SULFATE ION × 7 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP VAPOUR DIFFUSION IN 96-WELL PLATES AT 20 DEGREE C. 17 MG/ML PROTEIN IN 25 MM TRIS, PH 8, 20 MM NACL. RESERVOIR SOLUTION WAS 2M AMMONIUM SULFATE. DROPS WERE SET UP WITH EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION.	Resolution 1.93 Å R-free 0.205
4AW4 Engineered variant of Listeria monocytogenes InlB internalin domain with an additional leucine rich repeat inserted Deposited 2012-05-31	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 36–98（63 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321 Chain C 99–321（223 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP VAPOUR DIFFUSION IN 96-WELL PLATES AT 20 DEGREE C. 17 MG/ML PROTEIN IN 25 MM TRIS, PH 8, 20 MM NACL. RESERVOIR SOLUTION WAS 2M AMMONIUM SULFATE. DROPS WERE SET UP WITH EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION.	Resolution 1.93 Å R-free 0.205
6GCU MET receptor in complex with InlB internalin domain and DARPin A3A Deposited 2018-04-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 36–321（286 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.1 M HEPES sodium salt pH 7.5, 12% w/v PEG4000, protein complex concentration 5 mg/mL, equimolar ratio of macromolecules, drop size 0.2 uL, protein:reservoir ratio 1:1	Resolution 6.00 Å R-free 0.271
6GCU MET receptor in complex with InlB internalin domain and DARPin A3A Deposited 2018-04-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 36–321（286 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.1 M HEPES sodium salt pH 7.5, 12% w/v PEG4000, protein complex concentration 5 mg/mL, equimolar ratio of macromolecules, drop size 0.2 uL, protein:reservoir ratio 1:1	Resolution 6.00 Å R-free 0.271

16 other PDB entries and 34 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 59–287； UniProt 93–321

YOPM-CAP, INTERNALIN B

LISTERIA MONOCYTOGENES

UniProt P74988

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 34–87	Fragment：YOPM N-TERMINAL CAP RESIDUES 34-87, INLB LEUCINE-RICH REPEAT AND INTER-REPEAT REGION RESIDUES 93-321	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；HANGING DROP VAPOUR DIFFUSION AT 293 K WITH A DROP SIZE OF 2 UL CONSISTING OF EQUAL VOLUMES OF PROTEIN AT A CONCENTRATION OF 10 MG/ML AND RESERVOIR SOLUTION (0.1 M TRICINE, PH 9.0, 28% PEG 1000, 10% GLYCEROL, 0.25M KCL). CRYSTALS WERE CRYO-PROTECTED WITH RESERVOIR-SOLUTION ADDITIONALLY CONTAINING 15% GLYCEROL AND FLASH-FROZEN IN LIQUID NITROGEN	Resolution 1.50 Å R-free 0.219

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4CIL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8QP7 Crystal structure of Hepatitis C Virus E2 glycoprotein epitopeI 411-424 scaffold design 4CIL_04 Deposited 2023-09-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 34–78（45 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

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	P74988_YEREN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–58； UniProt 34–87

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4cil
Deposition date deposition_date	2013-12-11
Structure title title	YopM-InlB: Hybrid leucine-rich repeat protein
Keywords keywords	SIGNALING PROTEIN, CAPPING, FUSION PROTEIN, LRR, PROTEIN CHIMERA, PROTEIN DESIGN, PROTEIN ENGINEERING; SIGNALING PROTEIN
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	24.56 Å
Radius of gyration Rg (electron density) rg_electron	23.86 Å
Forward intensity I(0) i0	16412000.00
Molecular weight molecular_weight	31426.0 kDa
Excluded volume excluded_volume	39707 Å³
Envelope volume envelope_volume	47505 Å³
Hydration-shell volume shell_volume	18362 Å³
Envelope diameter envelope_diameter	85.6 Å
Shell Rg shell_rg	28.73 Å
Envelope Rg envelope_rg	24.22 Å
Shape Rg shape_rg	23.90 Å
Total Rg total_rg	24.41 Å
Total atoms total_atoms	2218
Residues n_residues	279
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	83.5 Å
Rg (real space) rg_real	24.87 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.6410e+07
I(0) uncertainty (real space) i0_real_error	2.4590e+05
Rg (reciprocal space) rg_reciprocal	24.79 Å
I(0) (reciprocal space) i0_reciprocal	16410000.0000
Solution quality estimate total_estimate	0.8112
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.559
Kurtosis Kurtosis kurtosis	-0.311
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2823000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.674; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.594; Smooth: 0.935

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4cilA01
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	4cilA02
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	59.210 Å
Unit-cell length b length_b	30.680 Å
Unit-cell length c length_c	135.390 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.98 °
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	1.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1771
R_work r_work	0.1749
R_free r_free	0.2187

Description description	YOPM-CAP, INTERNALIN B
Molecular weight formula_weight	32170.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2512

YopM-InlB: Hybrid leucine-rich repeat protein

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

YOPM-CAP, INTERNALIN B

State in the Current Structure

Other States of the Same Protein in the Database

YOPM-CAP, 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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	250

fit	/app/data/saxs_computation/ci/4cil/4cil.fit
pddf	/app/data/pr_computation/ci/4cil/4cil.pr.out
profile	/app/data/saxs_computation/ci/4cil/4cil.dat