1m54

CYSTATHIONINE-BETA SYNTHASE: REDUCED VICINAL THIOLS

Method: X-RAY DIFFRACTION D_max: 147.8 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	1m54
沉积日期 deposition_date	2002-07-08
结构标题 title	CYSTATHIONINE-BETA SYNTHASE: REDUCED VICINAL THIOLS
关键词 keywords	PLP PROTEIN FOLD TYPE II (TRYPTOPHAN SYNTHASE), PLP AND HEME BOUND TO PROTEIN, REDUCED VICINAL CYSTEINES, LYASE; LYASE
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	43.49 Å
回转半径 Rg (电子) rg_electron	43.45 Å
零角强度 I(0) i0	809980000.00
分子量 molecular_weight	232720.0 kDa
排除体积 excluded_volume	290870 Å³
包络体积 envelope_volume	371340 Å³
水化壳体积 shell_volume	71760 Å³
包络直径 envelope_diameter	156.7 Å
壳层 Rg shell_rg	47.41 Å
包络 Rg envelope_rg	43.48 Å
形状 Rg shape_rg	43.48 Å
总 Rg total_rg	43.52 Å
总原子数 total_atoms	16299
残基数 n_residues	2082
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	147.8 Å
Rg (实空间) rg_real	43.69 Å
Rg 误差 (实空间) rg_real_error	1.36 Å
I(0) (实空间) i0_real	8.1000e+08
I(0) 误差 (实空间) i0_real_error	1.5920e+07
Rg (倒空间) rg_reciprocal	43.50 Å
I(0) (倒空间) i0_reciprocal	809800000.0000
解质量估计 total_estimate	0.8445
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	45.2 Å
偏度 Skewness skewness	0.535
峰度 Kurtosis kurtosis	-0.061
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	174300000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.577

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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	CYSTATHIONINE BETA-SYNTHASE
分子量 formula_weight	39922.7 kDa
EC 编号 ec_number	4.2.1.22
突变 mutation	I44M
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	16403

MRPDAPSRCTWQLGRPASESPHHHTAPAKSPKILPDILKKIGDTPMVRINKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDTIIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPTNARFDSPESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPEELNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWMLQKGFLKEEDLTEKK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

Entity 2 non-polymer

描述 description	PYRIDOXAL-5'-PHOSPHATE
分子量 formula_weight	247.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 3 non-polymer

描述 description	PROTOPORPHYRIN IX CONTAINING FE
分子量 formula_weight	616.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	104

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1m54a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
超家族 Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
家族 Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

结构域编号 domain_id	d1m54b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
超家族 Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
家族 Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

结构域编号 domain_id	d1m54c_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
超家族 Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
家族 Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

结构域编号 domain_id	d1m54d_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
超家族 Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
家族 Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

结构域编号 domain_id	d1m54e_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
超家族 Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
家族 Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

结构域编号 domain_id	d1m54f_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
超家族 Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
家族 Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

CATH v4.4 (12 domains)

结构域编号 domain_id	1m54A01
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	1100 —

结构域编号 domain_id	1m54A02
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	1100 —

结构域编号 domain_id	1m54B01
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	1100 —

结构域编号 domain_id	1m54B02
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	1100 —

结构域编号 domain_id	1m54C01
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	1100 —

结构域编号 domain_id	1m54C02
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	1100 —

结构域编号 domain_id	1m54D01
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	1100 —

结构域编号 domain_id	1m54D02
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	1100 —

结构域编号 domain_id	1m54E01
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	1100 —

结构域编号 domain_id	1m54E02
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	1100 —

结构域编号 domain_id	1m54F01
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	1100 —

结构域编号 domain_id	1m54F02
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	1100 —

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7. 引用文献 (2)

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晶胞边长 a length_a	85.740 Å
晶胞边长 b length_b	85.626 Å
晶胞边长 c length_c	97.082 Å
晶胞夹角 α angle_alpha	102.01 °
晶胞夹角 β angle_beta	101.53 °
晶胞夹角 γ angle_gamma	112.60 °
晶胞分子数 Z z_pdb	6

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

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	—
R_work r_work	0.2710
R_free r_free	0.3650

fit	/app/data/saxs_computation/m5/1m54/1m54.fit
pddf	/app/data/pr_computation/m5/1m54/1m54.pr.out
profile	/app/data/saxs_computation/m5/1m54/1m54.dat