SAXSdb — 2gwc

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gwc
沉积日期 deposition_date	2006-05-04
结构标题 title	Crystal structure of plant glutamate cysteine ligase in complex with a transition state analogue
关键词 keywords	disulfide bridges, glutathione biosynthesis, beta-hairpin, redox regulation, 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	58.15 Å
回转半径 Rg (电子) rg_electron	58.27 Å
零角强度 I(0) i0	2413670000.00
分子量 molecular_weight	406910.0 kDa
排除体积 excluded_volume	504350 Å³
包络体积 envelope_volume	695970 Å³
水化壳体积 shell_volume	103710 Å³
包络直径 envelope_diameter	204.8 Å
壳层 Rg shell_rg	57.15 Å
包络 Rg envelope_rg	56.80 Å
形状 Rg shape_rg	58.26 Å
总 Rg total_rg	58.28 Å
总原子数 total_atoms	28122
残基数 n_residues	3353
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	189.0 Å
Rg (实空间) rg_real	58.29 Å
Rg 误差 (实空间) rg_real_error	1.29 Å
I(0) (实空间) i0_real	2.4140e+09
I(0) 误差 (实空间) i0_real_error	4.2120e+07
Rg (倒空间) rg_reciprocal	58.01 Å
I(0) (倒空间) i0_reciprocal	2413000000.0000
解质量估计 total_estimate	0.8533
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	70.0 Å
偏度 Skewness skewness	0.414
峰度 Kurtosis kurtosis	-0.166
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	64940000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.386

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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 (4)

Entity 1 polymer

描述 description	Glutamate cysteine ligase
分子量 formula_weight	51818.3 kDa
EC 编号 ec_number	6.3.2.2
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	29207

AASPPTEEAVVATEPLTREDLIAYLASGCKSKEKWRIGTEHEKFGFEVNTLRPMKYDQIAELLNSIAERFEWEKVMEGDKIIGLKQGKQSISLEPGGQFELSGAPLETLHQTCAEVNSHLYQVKAVAEEMGIGFLGMGFQPKWRREDIPTMPKGRYDIMRNYMPKVGSLGLDMMLRTCTVQVNLDFSSEADMIRKFRAGLALQPIATALFANSPFTEGKPNGFLSMRSHIWTDTDKDRTGMLPFVFDDSFGFEQYVDYALDVPMYFAYRNGKYVDCTGMTFRQFLAGKLPCLPGELPTYNDWENHLTTIFPEVRLKRYMEMRGADGGPWRRLCALPAFWVGLLYDEDVLQSVLDLTADWTPAEREMLRNKVPVTGLKTPFRDGLLKHVAEDVLKLAKDGLERRGYKEVGFLNAVTEVVRTGVTPAENLLEMYNGEWGQSVDPVFQELLY

来源 Source

来源生物 organism	Brassica juncea
NCBI 分类编号 ncbi_taxonomy_id	3707
宿主生物 host_organism	Escherichia coli

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	8

Entity 3 non-polymer

描述 description	(2S)-2-amino-4-(S-butylsulfonimidoyl)butanoic acid
分子量 formula_weight	222.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	1017

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	2gwcA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	590 — Creatine Kinase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2gwcB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	590 — Creatine Kinase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2gwcC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	590 — Creatine Kinase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2gwcD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	590 — Creatine Kinase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2gwcE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	590 — Creatine Kinase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2gwcF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	590 — Creatine Kinase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2gwcG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	590 — Creatine Kinase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2gwcH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	590 — Creatine Kinase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 —

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7. 引用文献 (1)

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晶胞边长 a length_a	88.040 Å
晶胞边长 b length_b	198.920 Å
晶胞边长 c length_c	114.970 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	99.66 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.180 Å
最低分辨率 resolution_low	99.500 Å
R 因子 r_factor	0.2000
R_work r_work	0.1979
R_free r_free	0.2413

fit	/app/data/saxs_computation/gw/2gwc/2gwc.fit
pddf	/app/data/pr_computation/gw/2gwc/2gwc.pr.out
profile	/app/data/saxs_computation/gw/2gwc/2gwc.dat

Crystal structure of plant glutamate cysteine ligase in complex with a transition state analogue

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