1o7d

The structure of the bovine lysosomal a-mannosidase suggests a novel mechanism for low pH activation

Method: X-RAY DIFFRACTION D_max: 102.3 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	1o7d
沉积日期 deposition_date	2002-10-30
结构标题 title	The structure of the bovine lysosomal a-mannosidase suggests a novel mechanism for low pH activation
关键词 keywords	HYDROLASE, GLYCOSYL HYDROLASE FAMILY 38, A-MANNOSIDASE, LYSOSOMAL; HYDROLASE
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	29.11 Å
回转半径 Rg (电子) rg_electron	28.33 Å
零角强度 I(0) i0	170401000.00
分子量 molecular_weight	104180.0 kDa
排除体积 excluded_volume	130470 Å³
包络体积 envelope_volume	153790 Å³
水化壳体积 shell_volume	43377 Å³
包络直径 envelope_diameter	106.1 Å
壳层 Rg shell_rg	37.09 Å
包络 Rg envelope_rg	28.87 Å
形状 Rg shape_rg	28.30 Å
总 Rg total_rg	29.22 Å
总原子数 total_atoms	7346
残基数 n_residues	898
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	102.3 Å
Rg (实空间) rg_real	29.04 Å
Rg 误差 (实空间) rg_real_error	0.58 Å
I(0) (实空间) i0_real	1.7040e+08
I(0) 误差 (实空间) i0_real_error	2.2460e+06
Rg (倒空间) rg_reciprocal	29.07 Å
I(0) (倒空间) i0_reciprocal	170400000.0000
解质量估计 total_estimate	0.8507
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	36.0 Å
偏度 Skewness skewness	0.355
峰度 Kurtosis kurtosis	-0.122
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	72940000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.688; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.992

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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 (12)

Entity 1 polymer

描述 description	Lysosomal alpha-mannosidase
分子量 formula_weight	34527.2 kDa
EC 编号 ec_number	3.2.1.24
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	7385

AGYKTCPKVKPDMLNVHLVPHTHDDVGWLKTVDQYFYGIYNNIQPAGVQYILDSVISSLLANPTRRFIYVEIAFFSRWWRQQTNATQKIVRELVRQGRLEFANGGWVMNDEATTHYGAIIDQMTLGLRFLEETFGSDGRPRVAWHIDPFGHSREQASLFAQMGFDGFFFGRLDYQDKKVRKKTLQMEQVWRASTSLKPPTADLFTSVLPNMYNPPEGLCWDMLCADKPVVEDTRSPEYNAKELVRYFLKLATDQGKLYRTKHTVMTMGSDFQYENANTWFKNLDKLIQLVNAQQRANG

Entity 2 polymer

描述 description	Lysosomal alpha-mannosidase
分子量 formula_weight	9649.9 kDa
EC 编号 ec_number	3.2.1.24
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

IRVNVLYSTPACYLWELNKANLSWSVKKDDFFPYADGPYMFWTGYFSSRPALKRYERLSYNFLQVCNQLEALAGPAANVGPYGS

Entity 3 polymer

描述 description	Lysosomal alpha-mannosidase
分子量 formula_weight	17596.1 kDa
EC 编号 ec_number	3.2.1.24
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

GDSAPLNEAMAVLQHHDAVSGTSRQHVANDYARQLSEGWRPCEVLMSNALAHLSGLKEDFAFCRKLNISICPLTQTAERFQVIVYNPLGRKVDWMVRLPVSKHVYLVKDPGGKIVPSDVVTIPSSDSQELLFSALVPAVGFSIYSVSQMPNQRPQKSWS

Entity 4 polymer

描述 description	Lysosomal alpha-mannosidase
分子量 formula_weight	32225.5 kDa
EC 编号 ec_number	3.2.1.24
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D

RDLVIQNEYLRARFDPNTGLLMELENLEQNLLLPVRQAFYWYNASTGNNLSSQASGAYIFRPNQNKPLFVSHWAQTHLVKASLVQEVHQNFSAWCSQVVRLYPRQRHLELEWTVGPIPVGDGWGKEVISRFDTALATRGLFYTDSNGREILERRRNYRPTWKLNQTEPVAGNYYPVNSRIYITDGNMQLTVLTDRSQGGSSLRDGSLELMVHRRLLKDDARGVGEPLNKEGSGLWVRGRHLVLLDKKETAAARHRLQAEMEVLAPQVVLAQGGGARYRLEKA

Entity 5 polymer

描述 description	Lysosomal alpha-mannosidase
分子量 formula_weight	14054.8 kDa
EC 编号 ec_number	3.2.1.24
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E

PRTQFSGLRRELPPSVRLLTLARWGPETLLLRLEHQFAVGEDSGRNLSSPVTLDLTNLFSAFTITNLRETTLAANQLLAYASRLQWTTDTGPTPHPSPSRPVSATITLQPMEIRTFLASVQWEEDG

Entity 6 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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	1559.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 7 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 8 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 9 non-polymer

描述 description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
分子量 formula_weight	122.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 10 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 11 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 12 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	39

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1o7d.1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
超家族 Superfamily superfamily	a.8.3 — Families 57/38 glycoside transferase middle domain
家族 Family family	a.8.3.1 — alpha-mannosidase, domain 2

结构域编号 domain_id	d1o7d.2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.30 — Supersandwich
超家族 Superfamily superfamily	b.30.5 — Galactose mutarotase-like
家族 Family family	b.30.5.6 — alpha-mannosidase, C-terminal domain

结构域编号 domain_id	d1o7d.3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.6 — 7-stranded beta/alpha barrel
超家族 Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
家族 Family family	c.6.2.1 — alpha-mannosidase

CATH v4.4 (6 domains)

结构域编号 domain_id	1o7dA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	110 — 7-stranded beta/alpha barrel
同源超家族 H-superfamily homologous superfamily	10 — Glycoside hydrolase 38, N terminal domain

结构域编号 domain_id	1o7dB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
同源超家族 H-superfamily homologous superfamily	50 — Glycoside hydrolase family 38, central domain

结构域编号 domain_id	1o7dC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
同源超家族 H-superfamily homologous superfamily	50 — Glycoside hydrolase family 38, central domain

结构域编号 domain_id	1o7dC02
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	1180 — Golgi alpha-mannosidase II

结构域编号 domain_id	1o7dD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily	30 — Golgi alpha-mannosidase II; domain 4

结构域编号 domain_id	1o7dE00
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	1360 —

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7. 引用文献 (2)

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晶胞边长 a length_a	117.880 Å
晶胞边长 b length_b	117.880 Å
晶胞边长 c length_c	582.040 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 61 2 2
空间群编号 int_tables_number	178
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2570
R_work r_work	0.2570
R_free r_free	0.2890

fit	/app/data/saxs_computation/o7/1o7d/1o7d.fit
pddf	/app/data/pr_computation/o7/1o7d/1o7d.pr.out
profile	/app/data/saxs_computation/o7/1o7d/1o7d.dat

The structure of the bovine lysosomal a-mannosidase suggests a novel mechanism for low pH activation

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

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

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (12)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 branched

Entity 7 branched

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 water

6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)