4cil

YopM-InlB: Hybrid leucine-rich repeat protein

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

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

YOPM-CAP, INTERNALIN B

LISTERIA MONOCYTOGENES

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	信息不足单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 A； UniProt 93–321	片段：YOPM N-TERMINAL CAP RESIDUES 34-87, INLB LEUCINE-RICH REPEAT AND INTER-REPEAT REGION RESIDUES 93-321	无其他共同聚合物	X-RAY DIFFRACTION X-ray结晶条件：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	分辨率 1.50 Å R-free 0.219

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 4CIL	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1D0B INTERNALIN B LEUCINE RICH REPEAT DOMAIN 提交 1999-09-09	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 36–248（213 aa）片段：LRR DOMAIN, RESIDUES 36-248	未记录	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 1.86 Å R-free 0.235
1H6T Internalin B: crystal structure of fused N-terminal domains. 提交 2001-06-22	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 36–321（286 aa）片段：LRR DOMAIN, RESIDUES 36-321	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 1.60 Å R-free 0.197
1M9S Crystal structure of Internalin B (InlB), a Listeria monocytogenes virulence protein containing SH3-like domains. 提交 2002-07-29	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 36–630（595 aa）	未记录	TB TERBIUM(III) ION × 7 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；lithium sulfate, glycerol, dithiothreitol, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.65 Å R-free 0.302
1OTM Calcium-binding mutant of the internalin B LRR domain 提交 2003-03-21	构建体不同突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 36–248（213 aa）片段：LRR domain	突变：D51A, D59A	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Peg 8000, Mes, Calcium acetate, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 1.93 Å R-free 0.240
1OTN Calcium-binding mutant of the Internalin B LRR domain 提交 2003-03-21	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 36–248（213 aa）片段：LRR domain	突变：D51A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Peg 8000, Mes, Calcium acetate, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 1.97 Å R-free 0.244
1OTO Calcium-binding mutant of the internalin B LRR domain 提交 2003-03-21	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 36–248（213 aa）片段：LRR domain	突变：D59A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Peg 8000, Mes, Calcium acetate, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 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 提交 2007-05-02	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 36–321（286 aa）片段：INTERNALIN DOMAIN (CAP, LRR, IR), INLB321, RESIDUES 36-320	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 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 提交 2007-05-02	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 C 36–321（286 aa）片段：INTERNALIN DOMAIN (CAP, LRR, IR), INLB321, RESIDUES 36-320	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 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 提交 2007-05-02	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 36–321（286 aa）片段：INTERNALIN DOMAIN (CAP, LRR, IR)\: INLB321, RESIDUES 36-321	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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)	分辨率 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 提交 2007-05-02	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 C 36–321（286 aa）片段：INTERNALIN DOMAIN (CAP, LRR, IR)\: INLB321, RESIDUES 36-321	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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)	分辨率 4.00 Å R-free 0.301
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form 提交 2009-08-27	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 36–321（286 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	未记录	SO4 SULFATE ION × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form 提交 2009-08-27	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 36–321（286 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	未记录	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form 提交 2009-08-27	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 36–321（286 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	未记录	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form 提交 2009-08-27	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 4 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 D 36–321（286 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form 提交 2009-08-27	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 5 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 E 36–321（286 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	未记录	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form 提交 2009-08-27	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 6 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 F 36–321（286 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	未记录	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 2.60 Å R-free 0.249
2WQV Internalin domain of Listeria monocytogenes InlB: rhombohedral crystal form 提交 2009-08-27	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 36–321（286 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	未记录	PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 2.80 Å R-free 0.238
2WQV Internalin domain of Listeria monocytogenes InlB: rhombohedral crystal form 提交 2009-08-27	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 36–321（286 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	未记录	PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 2.80 Å R-free 0.238
2WQW DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER of the Listeria monocytogenes InlB internalin domain 提交 2009-08-27	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 B 36–321（286 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	突变：YES	PEG DI(HYDROXYETHYL)ETHER × 12	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.24 Å R-free 0.239
2WQW DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER of the Listeria monocytogenes InlB internalin domain 提交 2009-08-27	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 36–321（286 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	突变：YES	PEG DI(HYDROXYETHYL)ETHER × 6	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.24 Å R-free 0.239
2WQX InlB321_4R: S199R, D200R, G206R, A227R, C242A mutant of the Listeria monocytogenes InlB internalin domain 提交 2009-08-27	构建体不同突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 36–321（286 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	突变：YES	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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).	分辨率 2.03 Å R-free 0.257
2WQX InlB321_4R: S199R, D200R, G206R, A227R, C242A mutant of the Listeria monocytogenes InlB internalin domain 提交 2009-08-27	构建体不同突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 36–321（286 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	突变：YES	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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).	分辨率 2.03 Å R-free 0.257
2Y5P B-repeat of Listeria monocytogenes InlB (internalin B) 提交 2011-01-17	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 322–392（71 aa）片段：B-REPEAT, RESIDUES 322-392	未记录	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 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).	分辨率 1.30 Å R-free 0.196
2Y5P B-repeat of Listeria monocytogenes InlB (internalin B) 提交 2011-01-17	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 322–392（71 aa）片段：B-REPEAT, RESIDUES 322-392	未记录	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 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).	分辨率 1.30 Å R-free 0.196
2Y5P B-repeat of Listeria monocytogenes InlB (internalin B) 提交 2011-01-17	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 322–392（71 aa）片段：B-REPEAT, RESIDUES 322-392	未记录	CA CALCIUM ION × 3 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 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).	分辨率 1.30 Å R-free 0.196
2Y5P B-repeat of Listeria monocytogenes InlB (internalin B) 提交 2011-01-17	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 4 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 D 322–392（71 aa）片段：B-REPEAT, RESIDUES 322-392	未记录	CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 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).	分辨率 1.30 Å R-free 0.196
2Y5P B-repeat of Listeria monocytogenes InlB (internalin B) 提交 2011-01-17	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 5 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 322–392（71 aa）片段：B-REPEAT, RESIDUES 322-392 链 B 322–392（71 aa）片段：B-REPEAT, RESIDUES 322-392 链 C 322–392（71 aa）片段：B-REPEAT, RESIDUES 322-392 链 D 322–392（71 aa）片段：B-REPEAT, RESIDUES 322-392	未记录	CA CALCIUM ION × 8 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray结晶条件 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).	分辨率 1.30 Å R-free 0.196
2Y5Q Listeria monocytogenes InlB (internalin B) residues 36-392 提交 2011-01-17	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 36–392（357 aa）片段：INTERNALIN DOMAIN AND B-REPEAT, RESIDUES 36-392	未记录	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray结晶条件 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).	分辨率 3.20 Å R-free 0.225
2Y5Q Listeria monocytogenes InlB (internalin B) residues 36-392 提交 2011-01-17	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 36–392（357 aa）片段：INTERNALIN DOMAIN AND B-REPEAT, RESIDUES 36-392	未记录	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray结晶条件 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).	分辨率 3.20 Å R-free 0.225
4AW4 Engineered variant of Listeria monocytogenes InlB internalin domain with an additional leucine rich repeat inserted 提交 2012-05-31	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 36–98（63 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321 链 A 99–321（223 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	未记录	SO4 SULFATE ION × 9 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 1.93 Å R-free 0.205
4AW4 Engineered variant of Listeria monocytogenes InlB internalin domain with an additional leucine rich repeat inserted 提交 2012-05-31	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 36–98（63 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321 链 B 99–321（223 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	未记录	SO4 SULFATE ION × 7 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 1.93 Å R-free 0.205
4AW4 Engineered variant of Listeria monocytogenes InlB internalin domain with an additional leucine rich repeat inserted 提交 2012-05-31	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 36–98（63 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321 链 C 99–321（223 aa）片段：INTERNALIN DOMAIN, RESIDUES 36-321	未记录	SO4 SULFATE ION × 6 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 1.93 Å R-free 0.205
6GCU MET receptor in complex with InlB internalin domain and DARPin A3A 提交 2018-04-19	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 B 36–321（286 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 6.00 Å R-free 0.271
6GCU MET receptor in complex with InlB internalin domain and DARPin A3A 提交 2018-04-19	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 E 36–321（286 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 6.00 Å R-free 0.271

共 16 个其他 PDB 条目、34 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	INLB_LISMO
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 59–287； UniProt 93–321

YOPM-CAP, INTERNALIN B

LISTERIA MONOCYTOGENES

UniProt P74988

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	信息不足单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 A； UniProt 34–87	片段：YOPM N-TERMINAL CAP RESIDUES 34-87, INLB LEUCINE-RICH REPEAT AND INTER-REPEAT REGION RESIDUES 93-321	无其他共同聚合物	X-RAY DIFFRACTION X-ray结晶条件：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	分辨率 1.50 Å R-free 0.219

数据库中的同蛋白其他状态

其他 PDB	相对当前条目 4CIL	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
8QP7 Crystal structure of Hepatitis C Virus E2 glycoprotein epitopeI 411-424 scaffold design 4CIL_04 提交 2023-09-30	构建体不同实验环境不同结构质量不同	Assembly 1 信息不足单体；蛋白 × 1 PDB 声明：monomeric	链 A 34–78（45 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；25% (w/v) PEG 1500, 100 mM MMT buffer pH 9.0	分辨率 2.05 Å R-free 0.262

共 1 个其他 PDB 条目、1 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	P74988_YEREN
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 5–58； UniProt 34–87

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

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

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	4cil
沉积日期 deposition_date	2013-12-11
结构标题 title	YopM-InlB: Hybrid leucine-rich repeat protein
关键词 keywords	SIGNALING PROTEIN, CAPPING, FUSION PROTEIN, LRR, PROTEIN CHIMERA, PROTEIN DESIGN, PROTEIN ENGINEERING; SIGNALING PROTEIN
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	24.56 Å
回转半径 Rg (电子) rg_electron	23.86 Å
零角强度 I(0) i0	16412000.00
分子量 molecular_weight	31426.0 kDa
排除体积 excluded_volume	39707 Å³
包络体积 envelope_volume	47505 Å³
水化壳体积 shell_volume	18362 Å³
包络直径 envelope_diameter	85.6 Å
壳层 Rg shell_rg	28.73 Å
包络 Rg envelope_rg	24.22 Å
形状 Rg shape_rg	23.90 Å
总 Rg total_rg	24.41 Å
总原子数 total_atoms	2218
残基数 n_residues	279
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	83.5 Å
Rg (实空间) rg_real	24.87 Å
Rg 误差 (实空间) rg_real_error	0.83 Å
I(0) (实空间) i0_real	1.6410e+07
I(0) 误差 (实空间) i0_real_error	2.4590e+05
Rg (倒空间) rg_reciprocal	24.79 Å
I(0) (倒空间) i0_reciprocal	16410000.0000
解质量估计 total_estimate	0.8112
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	21.2 Å
偏度 Skewness skewness	0.559
峰度 Kurtosis kurtosis	-0.311
角度范围 angular_range	— – 0.3250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2823000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 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. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (2)

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7. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	4cilA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	80 — Alpha-Beta Horseshoe
拓扑 Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease Inhibitor

结构域编号 domain_id	4cilA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1220 —

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8. 引用文献 (1)

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晶胞边长 a length_a	59.210 Å
晶胞边长 b length_b	30.680 Å
晶胞边长 c length_c	135.390 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.98 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1771
R_work r_work	0.1749
R_free r_free	0.2187

描述 description	YOPM-CAP, INTERNALIN B
分子量 formula_weight	32170.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合物类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	2512

YopM-InlB: Hybrid leucine-rich repeat protein

1. 蛋白身份与相关结构 Protein Identity & Related Structures

YOPM-CAP, INTERNALIN B

当前结构中的状态

数据库中的同蛋白其他状态

YOPM-CAP, INTERNALIN B

当前结构中的状态

数据库中的同蛋白其他状态

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

2. 结构基本信息 2. Structure Basics

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

5. 晶体学与实验 5. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

6. 实体与聚合物信息 Entities & Polymers (2)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 water

7. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)

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

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 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