SAXSdb — 2hre

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2hre
沉积日期 deposition_date	2006-07-20
结构标题 title	Structure of human ferrochelatase variant E343K with protoporphyrin IX bound
关键词 keywords	Heme synthesis, Ferrochelatase, Protoporphyrin IX, 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	44.81 Å
回转半径 Rg (电子) rg_electron	45.19 Å
零角强度 I(0) i0	406441000.00
分子量 molecular_weight	169410.0 kDa
排除体积 excluded_volume	213350 Å³
包络体积 envelope_volume	267440 Å³
水化壳体积 shell_volume	51979 Å³
包络直径 envelope_diameter	165.8 Å
壳层 Rg shell_rg	46.22 Å
包络 Rg envelope_rg	44.69 Å
形状 Rg shape_rg	45.20 Å
总 Rg total_rg	45.18 Å
总原子数 total_atoms	11890
残基数 n_residues	1436
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	157.8 Å
Rg (实空间) rg_real	45.33 Å
Rg 误差 (实空间) rg_real_error	1.66 Å
I(0) (实空间) i0_real	4.0640e+08
I(0) 误差 (实空间) i0_real_error	8.1780e+06
Rg (倒空间) rg_reciprocal	44.81 Å
I(0) (倒空间) i0_reciprocal	406200000.0000
解质量估计 total_estimate	0.7661
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	36.1 Å
偏度 Skewness skewness	0.538
峰度 Kurtosis kurtosis	-0.474
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	58450000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.586; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.513; Smooth: 0.683

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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	Ferrochelatase
分子量 formula_weight	41178.5 kDa
EC 编号 ec_number	4.99.1.1
突变 mutation	E343K
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	12228

RKPKTGILMLNMGGPETLGDVHDFLLRLFLDRDLMTLPIQNKLAPFIAKRRTPKIQEQYRRIGGGSPIKIWTSKQGEGMVKLLDELSPNTAPHKYYIGFRYVHPLTEEAIEEMERDGLERAIAFTQYPQYSCSTTGSSLNAIYRYYNQVGRKPTMKWSTIDRWPTHHLLIQCFADHILKELDHFPLEKRSEVVILFSAHSLPMSVVNRGDPYPQEVSATVQKVMERLEYCNPYRLVWQSKVGPMPWLGPQTDESIKGLCERGRKNILLVPIAFTSDHIKTLYELDIEYSQVLAKECGVENIRRAESLNGNPLFSKALADLVHSHIQSNELCSKQLTLSCPLCVNPVCRETKSFFTSQQL

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

Entity 2 non-polymer

描述 description	PROTOPORPHYRIN IX
分子量 formula_weight	562.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 3 non-polymer

描述 description	FE2/S2 (INORGANIC) CLUSTER
分子量 formula_weight	175.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	CHOLIC ACID
分子量 formula_weight	408.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	338

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2hrea_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.92 — Chelatase-like
超家族 Superfamily superfamily	c.92.1 — Chelatase
家族 Family family	c.92.1.1 — Ferrochelatase

结构域编号 domain_id	d2hreb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.92 — Chelatase-like
超家族 Superfamily superfamily	c.92.1 — Chelatase
家族 Family family	c.92.1.1 — Ferrochelatase

结构域编号 domain_id	d2hrec_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.92 — Chelatase-like
超家族 Superfamily superfamily	c.92.1 — Chelatase
家族 Family family	c.92.1.1 — Ferrochelatase

结构域编号 domain_id	d2hred_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.92 — Chelatase-like
超家族 Superfamily superfamily	c.92.1 — Chelatase
家族 Family family	c.92.1.1 — Ferrochelatase

CATH v4.4 (8 domains)

结构域编号 domain_id	2hreA01
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	1400 —

结构域编号 domain_id	2hreA02
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	1400 —

结构域编号 domain_id	2hreB01
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	1400 —

结构域编号 domain_id	2hreB02
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	1400 —

结构域编号 domain_id	2hreC01
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	1400 —

结构域编号 domain_id	2hreC02
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	1400 —

结构域编号 domain_id	2hreD01
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	1400 —

结构域编号 domain_id	2hreD02
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	1400 —

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7. 引用文献 (1)

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晶胞边长 a length_a	61.952 Å
晶胞边长 b length_b	88.388 Å
晶胞边长 c length_c	93.253 Å
晶胞夹角 α angle_alpha	102.41 °
晶胞夹角 β angle_beta	109.34 °
晶胞夹角 γ angle_gamma	105.58 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	43.660 Å
R 因子 r_factor	0.2160
R_work r_work	0.2160
R_free r_free	0.2790

fit	/app/data/saxs_computation/hr/2hre/2hre.fit
pddf	/app/data/pr_computation/hr/2hre/2hre.pr.out
profile	/app/data/saxs_computation/hr/2hre/2hre.dat

Structure of human ferrochelatase variant E343K with protoporphyrin IX bound

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