SAXSdb — 2y5p

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

INTERNALIN B

LISTERIA MONOCYTOGENES EGD

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	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 A； UniProt 322–392	片段：B-REPEAT, RESIDUES 322-392	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
2	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 B； UniProt 322–392	片段：B-REPEAT, RESIDUES 322-392	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
3	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 C； UniProt 322–392	片段：B-REPEAT, RESIDUES 322-392	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
4	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 D； UniProt 322–392	片段：B-REPEAT, RESIDUES 322-392	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
5	蛋白同源多聚体同源多聚体蛋白 × 4 PDB 声明：tetrameric（4）与蛋白拷贝数一致	链 A； UniProt 322–392 链 B； UniProt 322–392 链 C； UniProt 322–392 链 D； UniProt 322–392	片段：B-REPEAT, RESIDUES 322-392	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

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 2Y5P	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：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, 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配体/离子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配体/离子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配体/离子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配体/离子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 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	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	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
2Y5Q Listeria monocytogenes InlB (internalin B) residues 36-392 提交 2011-01-17	构建体不同配体/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
4CIL YopM-InlB: Hybrid leucine-rich repeat protein 提交 2013-12-11	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 信息不足单体；蛋白 × 1 PDB 声明：monomeric	链 A 93–321（229 aa）片段：YOPM N-TERMINAL CAP RESIDUES 34-87, INLB LEUCINE-RICH REPEAT AND INTER-REPEAT REGION RESIDUES 93-321	未记录	未记录非水小分子	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
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配体/离子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配体/离子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、30 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 4–74； UniProt 322–392 作者链 B； PDB构建体 4–74； UniProt 322–392 作者链 C； PDB构建体 4–74； UniProt 322–392 作者链 D； PDB构建体 4–74； UniProt 322–392

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。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	2y5p
沉积日期 deposition_date	2011-01-17
结构标题 title	B-repeat of Listeria monocytogenes InlB (internalin B)
关键词 keywords	PROTEIN BINDING, VIRULENCE FACTOR, PATHOGENICITY FACTOR, BETA-GRASP FOLD; PROTEIN BINDING
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	26.06 Å
回转半径 Rg (电子) rg_electron	25.60 Å
零角强度 I(0) i0	18271600.00
分子量 molecular_weight	33099.0 kDa
排除体积 excluded_volume	41575 Å³
包络体积 envelope_volume	53178 Å³
水化壳体积 shell_volume	19241 Å³
包络直径 envelope_diameter	87.3 Å
壳层 Rg shell_rg	30.08 Å
包络 Rg envelope_rg	25.80 Å
形状 Rg shape_rg	25.59 Å
总 Rg total_rg	26.23 Å
总原子数 total_atoms	2324
残基数 n_residues	289
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	85.3 Å
Rg (实空间) rg_real	26.36 Å
Rg 误差 (实空间) rg_real_error	0.63 Å
I(0) (实空间) i0_real	1.8270e+07
I(0) 误差 (实空间) i0_real_error	2.5170e+05
Rg (倒空间) rg_reciprocal	26.27 Å
I(0) (倒空间) i0_reciprocal	18270000.0000
解质量估计 total_estimate	0.8358
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	23.8 Å
偏度 Skewness skewness	0.564
峰度 Kurtosis kurtosis	-0.352
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2538000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.732; Smooth: 0.707

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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 (4)

实体 1 Entity 1 polymer

描述 description	INTERNALIN B
分子量 formula_weight	8303.2 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	2910

GAMVYTVSYDVDGTVIKTKVEAGTRITAPKPPTKQGYVFKGWYTEKNGGHEWNFNTDYMSGNDFTLYAVFKAET

来源 Source

来源生物 organism	LISTERIA MONOCYTOGENES EGD
NCBI 分类编号 ncbi_taxonomy_id	1334565
宿主生物 host_organism	ESCHERICHIA COLI

实体 2 Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

实体 3 Entity 3 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

实体 4 Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	396

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7. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

结构域编号 domain_id	2y5pA00
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	4270 — Listeria-Bacteroides repeat domain

结构域编号 domain_id	2y5pB00
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	4270 — Listeria-Bacteroides repeat domain

结构域编号 domain_id	2y5pC00
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	4270 — Listeria-Bacteroides repeat domain

结构域编号 domain_id	2y5pD00
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	4270 — Listeria-Bacteroides repeat domain

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8. 引用文献 (1)

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晶胞边长 a length_a	28.610 Å
晶胞边长 b length_b	58.340 Å
晶胞边长 c length_c	158.070 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.300 Å
最低分辨率 resolution_low	47.000 Å
R 因子 r_factor	0.1583
R_work r_work	0.1571
R_free r_free	0.1956

fit	/app/data/saxs_computation/y5/2y5p/2y5p.fit
pddf	/app/data/pr_computation/y5/2y5p/2y5p.pr.out
profile	/app/data/saxs_computation/y5/2y5p/2y5p.dat

B-repeat of Listeria monocytogenes InlB (internalin B)

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

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