9f40

Crystal structure of the NTD domain from S. cerevisia Niemann-Pick type C protein NCR1 with ergosterol bound

Method: X-RAY DIFFRACTION D_max: 126.1 Å Quality: GOOD

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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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9f40
沉积日期 deposition_date	2024-04-26
结构标题 title	Crystal structure of the NTD domain from S. cerevisia Niemann-Pick type C protein NCR1 with ergosterol bound
关键词 keywords	ergosterol, vacuole, NCR1, membrane protein, Niemann-Pick type C protein; MEMBRANE PROTEIN
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	36.19 Å
回转半径 Rg (电子) rg_electron	35.84 Å
零角强度 I(0) i0	229142000.00
分子量 molecular_weight	116020.0 kDa
排除体积 excluded_volume	142310 Å³
包络体积 envelope_volume	195770 Å³
水化壳体积 shell_volume	46791 Å³
包络直径 envelope_diameter	139.0 Å
壳层 Rg shell_rg	40.99 Å
包络 Rg envelope_rg	35.35 Å
形状 Rg shape_rg	35.83 Å
总 Rg total_rg	36.24 Å
总原子数 total_atoms	7969
残基数 n_residues	888
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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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	126.1 Å
Rg (实空间) rg_real	36.25 Å
Rg 误差 (实空间) rg_real_error	1.05 Å
I(0) (实空间) i0_real	2.2910e+08
I(0) 误差 (实空间) i0_real_error	4.0210e+06
Rg (倒空间) rg_reciprocal	36.22 Å
I(0) (倒空间) i0_reciprocal	229100000.0000
解质量估计 total_estimate	0.8652
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	45.9 Å
偏度 Skewness skewness	0.409
峰度 Kurtosis kurtosis	-0.097
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	40210000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.795; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.899

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (14)

Entity 1 polymer

描述 description	NPC intracellular sterol transporter 1-related protein 1
分子量 formula_weight	27809.8 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	8163

MNVLWIIALVGQLMRLVQGTATCAMYGNCGKKSVFGNELPCPVPRSFEPPVLSDETSKLLVEVCGEEWKEVRYACCTKDQVVALRDNLQKAQPLISSCPACLKNFNNLFCHFTCAADQGRFVNITKVEKSKEDKDIVAELDVFMNSSWASEFYDSCKNIKFSATNGYAMDLIGGGAKNYSQFLKFLGDAKPMLGGSPFQINYKYDLANEEKEWQEFNDEVYACDDAQYKCACSDCQESCPHLKPLVPR

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1235.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 4 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1073.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1073.0 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 6 branched

描述 description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 7 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 8 branched

描述 description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 9 non-polymer

描述 description	ERGOSTEROL
分子量 formula_weight	396.6 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 10 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	man
拷贝数 entity_count	9

Entity 11 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	man
拷贝数 entity_count	29

Entity 12 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	man
拷贝数 entity_count	12

Entity 13 non-polymer

描述 description	ACETONITRILE
分子量 formula_weight	41.1 kDa
来源方法 src_method	man
拷贝数 entity_count	9

Entity 14 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	194

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7. 引用文献 (1)

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晶胞边长 a length_a	92.760 Å
晶胞边长 b length_b	109.580 Å
晶胞边长 c length_c	151.810 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 2 21
空间群编号 int_tables_number	18
晶系 crystal_system	orthorhombic

分辨率 resolution	2.440 Å
最低分辨率 resolution_low	45.050 Å
R 因子 r_factor	0.2159
R_work r_work	0.2143
R_free r_free	0.2572

fit	/app/data/saxs_computation/f4/9f40/9f40.fit
pddf	/app/data/pr_computation/f4/9f40/9f40.pr.out
profile	/app/data/saxs_computation/f4/9f40/9f40.dat