2hbs

THE HIGH RESOLUTION CRYSTAL STRUCTURE OF DEOXYHEMOGLOBIN S

Method: X-RAY DIFFRACTION D_max: 117.9 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	2hbs
沉积日期 deposition_date	1997-05-06
结构标题 title	THE HIGH RESOLUTION CRYSTAL STRUCTURE OF DEOXYHEMOGLOBIN S
关键词 keywords	OXYGEN TRANSPORT, HEMOGLOBIN; OXYGEN TRANSPORT
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	37.09 Å
回转半径 Rg (电子) rg_electron	36.68 Å
零角强度 I(0) i0	233293000.00
分子量 molecular_weight	128790.0 kDa
排除体积 excluded_volume	163110 Å³
包络体积 envelope_volume	205010 Å³
水化壳体积 shell_volume	47332 Å³
包络直径 envelope_diameter	121.8 Å
壳层 Rg shell_rg	42.29 Å
包络 Rg envelope_rg	36.00 Å
形状 Rg shape_rg	36.66 Å
总 Rg total_rg	37.11 Å
总原子数 total_atoms	9104
残基数 n_residues	1148
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	117.9 Å
Rg (实空间) rg_real	37.21 Å
Rg 误差 (实空间) rg_real_error	0.76 Å
I(0) (实空间) i0_real	2.3330e+08
I(0) 误差 (实空间) i0_real_error	3.6190e+06
Rg (倒空间) rg_reciprocal	37.14 Å
I(0) (倒空间) i0_reciprocal	233300000.0000
解质量估计 total_estimate	0.8520
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	38.4 Å
偏度 Skewness skewness	0.388
峰度 Kurtosis kurtosis	-0.573
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	48250000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.509

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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	HEMOGLOBIN S (DEOXY), ALPHA CHAIN
分子量 formula_weight	15150.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G
原子数 atom_count	9677

VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

Entity 2 polymer

描述 description	HEMOGLOBIN S (DEOXY), BETA CHAIN
分子量 formula_weight	15860.2 kDa
突变 mutation	E6V VARIANT
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H

VHLTPVEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH

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	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	573

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2hbsa_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.1 — Globin-like
超家族 Superfamily superfamily	a.1.1 — Globin-like
家族 Family family	a.1.1.2 — Globins

结构域编号 domain_id	d2hbsb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.1 — Globin-like
超家族 Superfamily superfamily	a.1.1 — Globin-like
家族 Family family	a.1.1.2 — Globins

结构域编号 domain_id	d2hbsc_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.1 — Globin-like
超家族 Superfamily superfamily	a.1.1 — Globin-like
家族 Family family	a.1.1.2 — Globins

结构域编号 domain_id	d2hbsd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.1 — Globin-like
超家族 Superfamily superfamily	a.1.1 — Globin-like
家族 Family family	a.1.1.2 — Globins

结构域编号 domain_id	d2hbse_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.1 — Globin-like
超家族 Superfamily superfamily	a.1.1 — Globin-like
家族 Family family	a.1.1.2 — Globins

结构域编号 domain_id	d2hbsf_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.1 — Globin-like
超家族 Superfamily superfamily	a.1.1 — Globin-like
家族 Family family	a.1.1.2 — Globins

结构域编号 domain_id	d2hbsg_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.1 — Globin-like
超家族 Superfamily superfamily	a.1.1 — Globin-like
家族 Family family	a.1.1.2 — Globins

结构域编号 domain_id	d2hbsh_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.1 — Globin-like
超家族 Superfamily superfamily	a.1.1 — Globin-like
家族 Family family	a.1.1.2 — Globins

CATH v4.4 (8 domains)

结构域编号 domain_id	2hbsA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	490 — Globin-like
同源超家族 H-superfamily homologous superfamily	10 — Globins

结构域编号 domain_id	2hbsB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	490 — Globin-like
同源超家族 H-superfamily homologous superfamily	10 — Globins

结构域编号 domain_id	2hbsC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	490 — Globin-like
同源超家族 H-superfamily homologous superfamily	10 — Globins

结构域编号 domain_id	2hbsD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	490 — Globin-like
同源超家族 H-superfamily homologous superfamily	10 — Globins

结构域编号 domain_id	2hbsE00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	490 — Globin-like
同源超家族 H-superfamily homologous superfamily	10 — Globins

结构域编号 domain_id	2hbsF00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	490 — Globin-like
同源超家族 H-superfamily homologous superfamily	10 — Globins

结构域编号 domain_id	2hbsG00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	490 — Globin-like
同源超家族 H-superfamily homologous superfamily	10 — Globins

结构域编号 domain_id	2hbsH00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	490 — Globin-like
同源超家族 H-superfamily homologous superfamily	10 — Globins

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7. 引用文献 (7)

The high resolution crystal structure of deoxyhemoglobin S.

J.Mol.Biol. (1997)

PMID: 9325099 · DOI: 10.1006/jmbi.1997.1253 PRIMARY

Refined Crystal Structure of Deoxyhemoglobin S. II. Molecular Interactions in the Crystal

J.Biol.Chem. (1985)

Refined Crystal Structure of Deoxyhemoglobin S. I. Restrained Least-Squares Refinement at 3.0-A Resolution

J.Biol.Chem. (1985)

Intermolecular Interactions in Crystals of Human Deoxy Hemoglobin A, C, F and S

Inserm Symp. (1978)

Crystal Structure of Sickle-Cell Deoxyhemoglobin

;Proceedings of the Symposium on Molecular and Cellular Aspects of Sickle Cell Disease, Dallas, Texas, December 10, 1975 (in: Dhew Pub (Nih) (Us), No.76-1007) ; (1976)

Crystals of Deoxy Sickle Cell Hemoglobin

;Proceedings of the First National Symposium on Sickle Cell Disease, Washington, D.C., June 27-29, 1974 (in: Dhew Pub (Nih) (Us), No.75-723) ; (1975)

Crystal Structure of Sickle-Cell Deoxyhemoglobin at 5 A Resolution

J.Mol.Biol. (1975)

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晶胞边长 a length_a	63.344 Å
晶胞边长 b length_b	185.681 Å
晶胞边长 c length_c	52.933 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	92.74 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.050 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.1650
R_work r_work	0.1650
R_free r_free	0.2150

fit	/app/data/saxs_computation/hb/2hbs/2hbs.fit
pddf	/app/data/pr_computation/hb/2hbs/2hbs.pr.out
profile	/app/data/saxs_computation/hb/2hbs/2hbs.dat

THE HIGH RESOLUTION CRYSTAL STRUCTURE OF DEOXYHEMOGLOBIN S

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

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (7)

8. 文件与曲线 (10)

Files (7)

Curves (3)