9ep0

Dolichyl phosphate mannose synthase in complex with donor (GDP-Man) and traces of acceptor (Dol55P) and product (Dol55P-Man)

Method: X-RAY DIFFRACTION D_max: 94.5 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	9ep0
沉积日期 deposition_date	2024-03-16
结构标题 title	Dolichyl phosphate mannose synthase in complex with donor (GDP-Man) and traces of acceptor (Dol55P) and product (Dol55P-Man)
关键词 keywords	;Dolichyl phosphate mannose synthase, enzyme, integral membrane protein, protein glycosylation, glycosylphosphatidylinositol synthesis, GDP-mannose, dolichyl monophosphate, dolichol monophosphate mannose, donor-acceptor and product complex, TRANSFERASE ;; TRANSFERASE
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	25.69 Å
回转半径 Rg (电子) rg_electron	25.62 Å
零角强度 I(0) i0	23857400.00
分子量 molecular_weight	40470.0 kDa
排除体积 excluded_volume	52077 Å³
包络体积 envelope_volume	63244 Å³
水化壳体积 shell_volume	22332 Å³
包络直径 envelope_diameter	96.6 Å
壳层 Rg shell_rg	30.38 Å
包络 Rg envelope_rg	25.88 Å
形状 Rg shape_rg	25.66 Å
总 Rg total_rg	26.10 Å
总原子数 total_atoms	2859
残基数 n_residues	343
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	94.5 Å
Rg (实空间) rg_real	25.95 Å
Rg 误差 (实空间) rg_real_error	0.94 Å
I(0) (实空间) i0_real	2.3860e+07
I(0) 误差 (实空间) i0_real_error	3.6750e+05
Rg (倒空间) rg_reciprocal	25.87 Å
I(0) (倒空间) i0_reciprocal	23860000.0000
解质量估计 total_estimate	0.7955
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	25.9 Å
偏度 Skewness skewness	0.606
峰度 Kurtosis kurtosis	-0.106
角度范围 angular_range	— – 0.3100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2418000.0000
实空间数据点数 n_real_points	63
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.572; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.653; Smooth: 0.970

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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 (5)

Entity 1 polymer

描述 description	Dolichol monophosphate mannose synthase
分子量 formula_weight	42684.8 kDa
来源方法 src_method	man
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	2859

MHHHHHHSSGVDLGTENLYFQSMKVSVIIPTYNERENLEELFSRIDNALQGLNYEIVVVDDDSPDRTWEKAQELSSKYPVKVIRRTKEKGLSSAVIRGFKEASGDVFVVMDADLQHPPEVIPKLIEAIKNGSDIAIGSRYVKGGKVENWPFYRKLISKGAIMVGRIALPKIRDIKDPVSGFFALRKEVVEGVELNPIGFKILMEILIKGKYSKVVEVPFTFGIRARGESKLKGKTIFEYLRHIYRLMKWEGEIDRIVKFSIVGLSGILVNEGFLWLFVNLGIPKEIAVIPAVELSILNNFFWNDIWTFKDIRRGSIFSRLLKFHIAALSGAVVNFIVYWILLFLGIHYLIANLVGIVLSFGVRYVINRHVTWAT

来源 Source

来源生物 organism	Pyrococcus furiosus DSM 3638
NCBI 分类编号 ncbi_taxonomy_id	186497
宿主生物 host_organism	Escherichia coli B

Entity 2 non-polymer

描述 description	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
分子量 formula_weight	605.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	ETHYL DIHYDROGEN PHOSPHATE
分子量 formula_weight	126.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	dolichyl phosphate mannose
分子量 formula_weight	1011.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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晶胞边长 a length_a	87.800 Å
晶胞边长 b length_b	145.250 Å
晶胞边长 c length_c	99.020 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	8

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	43.900 Å
R 因子 r_factor	0.2429
R_work r_work	0.2369
R_free r_free	0.3006

fit	/app/data/saxs_computation/ep/9ep0/9ep0.fit
pddf	/app/data/pr_computation/ep/9ep0/9ep0.pr.out
profile	/app/data/saxs_computation/ep/9ep0/9ep0.dat

Dolichyl phosphate mannose synthase in complex with donor (GDP-Man) and traces of acceptor (Dol55P) and product (Dol55P-Man)

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