SAXSdb — 1hmo

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hmo
沉积日期 deposition_date	1990-10-18
结构标题 title	THE STRUCTURE OF DEOXY AND OXY HEMERYTHRIN AT 2.0 ANGSTROMS RESOLUTION
关键词 keywords	OXYGEN TRANSPORT; 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	30.21 Å
回转半径 Rg (电子) rg_electron	29.79 Å
零角强度 I(0) i0	48791800.00
分子量 molecular_weight	54199.0 kDa
排除体积 excluded_volume	67346 Å³
包络体积 envelope_volume	85219 Å³
水化壳体积 shell_volume	25658 Å³
包络直径 envelope_diameter	102.5 Å
壳层 Rg shell_rg	34.36 Å
包络 Rg envelope_rg	29.51 Å
形状 Rg shape_rg	29.80 Å
总 Rg total_rg	30.22 Å
总原子数 total_atoms	3816
残基数 n_residues	452
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	102.4 Å
Rg (实空间) rg_real	30.38 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	4.8790e+07
I(0) 误差 (实空间) i0_real_error	8.5560e+05
Rg (倒空间) rg_reciprocal	30.31 Å
I(0) (倒空间) i0_reciprocal	48790000.0000
解质量估计 total_estimate	0.8581
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	25.6 Å
偏度 Skewness skewness	0.385
峰度 Kurtosis kurtosis	-0.501
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5302000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.717; Smooth: 0.891

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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	HEMERYTHRIN
分子量 formula_weight	13369.0 kDa
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	4119

GFPIPDPYCWDISFRTFYTIIDDEHKTLFNGILLLSQADNADHLNELRRCTGKHFLNEQQLMQSSQYAGYAEHKKAHDDFIHKLDTWDGDVTYAKNWLVNHIKTIDFKYRGKI

来源 Source

来源生物 organism	Themiste dyscritum
NCBI 分类编号 ncbi_taxonomy_id	6436

Entity 2 non-polymer

描述 description	ACETYL GROUP
分子量 formula_weight	44.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	MU-OXO-DIIRON
分子量 formula_weight	127.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	OXYGEN MOLECULE
分子量 formula_weight	32.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	282

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1hmoa_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.4 — Hemerythrin-like
家族 Family family	a.24.4.1 — Hemerythrin-like

结构域编号 domain_id	d1hmob_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.4 — Hemerythrin-like
家族 Family family	a.24.4.1 — Hemerythrin-like

结构域编号 domain_id	d1hmoc_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.4 — Hemerythrin-like
家族 Family family	a.24.4.1 — Hemerythrin-like

结构域编号 domain_id	d1hmod_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.4 — Hemerythrin-like
家族 Family family	a.24.4.1 — Hemerythrin-like

CATH v4.4 (4 domains)

结构域编号 domain_id	1hmoA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	50 — Hemerythrin-like

结构域编号 domain_id	1hmoB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	50 — Hemerythrin-like

结构域编号 domain_id	1hmoC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	50 — Hemerythrin-like

结构域编号 domain_id	1hmoD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	50 — Hemerythrin-like

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7. 引用文献 (12)

Structures of deoxy and oxy hemerythrin at 2.0 A resolution.

J.Mol.Biol. (1991)

PMID: 2016748 · DOI: 10.1016/0022-2836(91)90703-9 PRIMARY

Active Site Structures of Deoxyhemerythrin and Oxyhemerythrin

Proc.Natl.Acad.Sci.USA (1985)

Binuclear Iron Complexes in Methemerythrin and Azidomethemerythrin at 2.0-Angstroms Resolution

J.Am.Chem.Soc. (1984)

Adjustment of Restraints in the Refinement of Methemerythrin and Azidomethemerythrin at 2.0 Angstroms Resolution.

Acta Crystallogr.,Sect.B (1983)

Restrained Least-Squares Refinement of Themiste Dyscritum Methydroxohemerythrin at 2.0 Angstroms Resolution

Acta Crystallogr.,Sect.B (1982)

Structure of the Binuclear Iron Complex in Metazidohaemerythrin from Themiste Dyscritum at 2.2 Angstroms Resolution

Nature (1981)

Amino Acid Sequence of Hemerythrin from Themiste Dyscritum.

J.Biol.Chem. (1978)

Crystallographic Studies of Azide, Thiocyanate and Perchlorate Complexes of Methemerythrin

J.Mol.Biol. (1978)

Structure of Methemerythrin at 2.8-Angstroms Resolution. Computer Graphics Fit of an Averaged Electron Density Map

Biochemistry (1978)

Structure of the Iron Complex in Methemerythrin

Proc.Natl.Acad.Sci.USA (1976)

Structure of Methemerythrin at 5 Angstroms Resolution

J.Mol.Biol. (1976)

An X-Ray Crystallographic Study of Hemerythrin

J.Mol.Biol. (1975)

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晶胞边长 a length_a	86.690 Å
晶胞边长 b length_b	86.690 Å
晶胞边长 c length_c	80.780 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	P 4
空间群编号 int_tables_number	75
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.1730
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/hm/1hmo/1hmo.fit
pddf	/app/data/pr_computation/hm/1hmo/1hmo.pr.out
profile	/app/data/saxs_computation/hm/1hmo/1hmo.dat

THE STRUCTURE OF DEOXY AND OXY HEMERYTHRIN AT 2.0 ANGSTROMS RESOLUTION

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution