1m0w

Yeast Glutathione Synthase Bound to gamma-glutamyl-cysteine, AMP-PNP and 2 Magnesium Ions

Method: X-RAY DIFFRACTION D_max: 111.4 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	1m0w
沉积日期 deposition_date	2002-06-14
结构标题 title	Yeast Glutathione Synthase Bound to gamma-glutamyl-cysteine, AMP-PNP and 2 Magnesium Ions
关键词 keywords	;Amine/Carboxylate Ligase, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, LIGASE ;; LIGASE
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	33.25 Å
回转半径 Rg (电子) rg_electron	32.98 Å
零角强度 I(0) i0	183097000.00
分子量 molecular_weight	109320.0 kDa
排除体积 excluded_volume	136890 Å³
包络体积 envelope_volume	168030 Å³
水化壳体积 shell_volume	42779 Å³
包络直径 envelope_diameter	119.5 Å
壳层 Rg shell_rg	39.38 Å
包络 Rg envelope_rg	33.14 Å
形状 Rg shape_rg	32.98 Å
总 Rg total_rg	33.43 Å
总原子数 total_atoms	7703
残基数 n_residues	960
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	111.4 Å
Rg (实空间) rg_real	33.42 Å
Rg 误差 (实空间) rg_real_error	0.89 Å
I(0) (实空间) i0_real	1.8310e+08
I(0) 误差 (实空间) i0_real_error	3.0760e+06
Rg (倒空间) rg_reciprocal	33.36 Å
I(0) (倒空间) i0_reciprocal	183100000.0000
解质量估计 total_estimate	0.8648
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	32.5 Å
偏度 Skewness skewness	0.468
峰度 Kurtosis kurtosis	-0.337
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	155500000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.932; Smooth: 0.870

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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 (6)

Entity 1 polymer

描述 description	glutathione synthetase
分子量 formula_weight	55878.9 kDa
EC 编号 ec_number	6.3.2.3
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	8810

MAHYPPSKDQLNELIQEVNQWAITNGLSMYPPKFEENPSNASVSPVTIYPTPIPRKCFDEAVQIQPVFNELYARITQDMAQPDSYLHKTTEALALSDSEFTGKLWSLYLATLKSAQYKKQNFRLGIFRSDYLIDKKKGTEQIKQVEFNTVSVSFAGLSEKVDRLHSYLNRANKYDPKGPIYNDQNMVISDSGYLLSKALAKAVESYKSQQSSSTTSDPIVAFIVQRNERNVFDQKVLELNLLEKFGTKSVRLTFDDVNDKLFIDDKTGKLFIRDTEQEIAVVYYRTGYTTTDYTSEKDWEARLFLEKSFAIKAPDLLTQLSGSKKIQQLLTDEGVLGKYISDAEKKSSLLKTFVKIYPLDDTKLGREGKRLALSEPSKYVLKPQREGGGNNVYKENIPNFLKGIEERHWDAYILMELIEPELNENNIILRDNKSYNEPIISELGIYGCVLFNDEQVLSNEFSGSLLRSKFNTSNEGGVAAGFGCLDSIILY

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21

Entity 2 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	4

Entity 3 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	7

Entity 4 non-polymer

描述 description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
分子量 formula_weight	506.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	GAMMA-GLUTAMYLCYSTEINE
分子量 formula_weight	250.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 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	747

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1m0wa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.30 — PreATP-grasp domain
超家族 Superfamily superfamily	c.30.1 — PreATP-grasp domain
家族 Family family	c.30.1.4 — Eukaryotic glutathione synthetase, substrate-binding domain

结构域编号 domain_id	d1m0wa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.142 — ATP-grasp
超家族 Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
家族 Family family	d.142.1.6 — Eukaryotic glutathione synthetase ATP-binding domain

结构域编号 domain_id	d1m0wb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.30 — PreATP-grasp domain
超家族 Superfamily superfamily	c.30.1 — PreATP-grasp domain
家族 Family family	c.30.1.4 — Eukaryotic glutathione synthetase, substrate-binding domain

结构域编号 domain_id	d1m0wb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.142 — ATP-grasp
超家族 Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
家族 Family family	d.142.1.6 — Eukaryotic glutathione synthetase ATP-binding domain

CATH v4.4 (10 domains)

结构域编号 domain_id	1m0wA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	80 —

结构域编号 domain_id	1m0wA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	20 — ATP-grasp fold, B domain

结构域编号 domain_id	1m0wA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1080 — Glutathione Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Glutathione Synthetase; Chain A, domain 3

结构域编号 domain_id	1m0wA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1760 — Glutathione synthase, substrate-binding domain superfamily, eukaryotic

结构域编号 domain_id	1m0wA05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	50 — Glutathione synthase lid domain

结构域编号 domain_id	1m0wB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	80 —

结构域编号 domain_id	1m0wB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	20 — ATP-grasp fold, B domain

结构域编号 domain_id	1m0wB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1080 — Glutathione Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Glutathione Synthetase; Chain A, domain 3

结构域编号 domain_id	1m0wB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1760 — Glutathione synthase, substrate-binding domain superfamily, eukaryotic

结构域编号 domain_id	1m0wB05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	50 — Glutathione synthase lid domain

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7. 引用文献 (1)

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晶胞边长 a length_a	51.661 Å
晶胞边长 b length_b	52.006 Å
晶胞边长 c length_c	100.636 Å
晶胞夹角 α angle_alpha	82.08 °
晶胞夹角 β angle_beta	86.77 °
晶胞夹角 γ angle_gamma	77.49 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1720
R_work r_work	0.1720
R_free r_free	0.1960

fit	/app/data/saxs_computation/m0/1m0w/1m0w.fit
pddf	/app/data/pr_computation/m0/1m0w/1m0w.pr.out
profile	/app/data/saxs_computation/m0/1m0w/1m0w.dat