1gdl

CRYSTAL STRUCTURE OF FERRIC COMPLEXES OF THE YELLOW LUPIN LEGHEMOGLOBIN WITH ISOQUINOLINE AT 1.8 ANGSTROMS RESOLUTION (RUSSIAN)

Method: X-RAY DIFFRACTION D_max: 50.2 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	1gdl
沉积日期 deposition_date	1994-09-14
结构标题 title	CRYSTAL STRUCTURE OF FERRIC COMPLEXES OF THE YELLOW LUPIN LEGHEMOGLOBIN WITH ISOQUINOLINE AT 1.8 ANGSTROMS RESOLUTION (RUSSIAN)
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	16.35 Å
回转半径 Rg (电子) rg_electron	14.84 Å
零角强度 I(0) i0	5119190.00
分子量 molecular_weight	17279.0 kDa
排除体积 excluded_volume	22034 Å³
包络体积 envelope_volume	24016 Å³
水化壳体积 shell_volume	13681 Å³
包络直径 envelope_diameter	49.5 Å
壳层 Rg shell_rg	20.71 Å
包络 Rg envelope_rg	15.06 Å
形状 Rg shape_rg	14.81 Å
总 Rg total_rg	16.09 Å
总原子数 total_atoms	1222
残基数 n_residues	153
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	50.2 Å
Rg (实空间) rg_real	16.23 Å
Rg 误差 (实空间) rg_real_error	0.23 Å
I(0) (实空间) i0_real	5.1190e+06
I(0) 误差 (实空间) i0_real_error	5.5830e+04
Rg (倒空间) rg_reciprocal	16.24 Å
I(0) (倒空间) i0_reciprocal	5119000.0000
解质量估计 total_estimate	0.8996
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	21.9 Å
偏度 Skewness skewness	0.093
峰度 Kurtosis kurtosis	-0.490
角度范围 angular_range	— – 0.4850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1348000.0000
实空间数据点数 n_real_points	79
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.984

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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	LEGHEMOGLOBIN (NITROGEN MONOXY)
分子量 formula_weight	16674.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	1390

GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLEVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELAIVIKKEMDDAA

来源 Source

来源生物 organism	Lupinus luteus
通用名 common_name	yellow lupine
NCBI 分类编号 ncbi_taxonomy_id	3873

Entity 2 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	1

Entity 3 non-polymer

描述 description	NITRIC OXIDE
分子量 formula_weight	30.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	163

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1gdla_
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 (1 domains)

结构域编号 domain_id	1gdlA00
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 (20)

The binding of carbon monoxide and nitric oxide to leghaemoglobin in comparison with other haemoglobins.

J.Mol.Biol. (1996)

PMID: 8950274 · DOI: 10.1006/jmbi.1996.0630 PRIMARY

X-Ray Structure of Ferrous Complexes of the Yellow Lupin Leghemoglobin with Co and No at 1.8 Angstroms Resolution (Russian)

Bioorg.Khim. (1988)

;X-Ray Structural Investigation of Leghemoglobin. Vi. Structure of Acetate-Ferrileghemoglobin at a Resolution of 2.0 Angstroms (Russian) ;

Kristallografiya (1980)

X-Ray Structural Investigation of Leghemoglobin. Vi. Structure of Acetate-Ferrileghemoglobin at a Resolution of 2.0 Angstroms

Sov.Phys.Crystallogr.(Engl.Transl.) (1980)

X-Ray Diffraction Study of Leghemoglobin. Iv. Determination of the Structure with 2.8 Angstroms Resolution (Russian)

Kristallografiya (1978)

X-Ray Structural Investigation of Leghemoglobin. Iv. Structure Determination at a Resolution of 2.8 Angstroms

Sov.Phys.Crystallogr.(Engl.Transl.) (1978)

Spatial Structure of Lupine Leghemoglobin with the 2.8 Angstroms Resolution (Russian)

Dokl.Akad.Nauk Sssr (1977)

Three-Dimensional Structure of Lupine Leghemoglobin with a Resolution of 2.8 Angstroms

Dokl.Biochem.(Engl.Transl.) (1977)

X-Ray Structural Study of Leghemoglobin. III. Crystallographic Data on the Structure of the First Component (Russian)

Kristallografiya (1977)

X-Ray Structural Study of Leghemoglobin. III. Crystallographic Data Regarding the Structure of the First Component

Sov.Phys.Crystallogr.(Engl.Transl.) (1977)

The Haem-Accessibility in Leghaemoglobin of Lupinus Luteus as Observed by Proton Magnetic Relaxation

Int.J.Pept.Protein Res. (1976)

X-Ray Study of Leghemoglobin. II. Determination of the Structure with Resolution of 5 Angstroms

Sov.Phys.Crystallogr.(Engl.Transl.) (1975)

X-Ray Study of Leghemoglobin. I.Purification, Crystallization, and Preparation of Derivatives Containing Heavy Atoms

Sov.Phys.Crystallogr.(Engl.Transl.) (1975)

Structure of Leghaemoglobin from Lupin Root Nodules at 5 Angstroms Resolution

Nature (1975)

The X-Ray Structural Study of Leghemoglobin. II. Determination of the Structure at 5 Angstroms Resolution (Russian)

Kristallografiya (1974)

;The X-Ray Structural Study of Leghemoglobin. I. Purification, Crystallization, and Production of Derivatives Containing Heavy Atoms (Russian) ;

Kristallografiya (1974)

X-Ray Determination of Three-Dimensional Structure of Leghemoglobin from Lupinus Luteus L. At 5 Angstroms Resolution (Russian)

Dokl.Akad.Nauk Sssr (1974)

;X-Ray Diffraction Determination of the Three-Dimensional Structure of Leghemoglobin of Lupinus Luteus L. With 5 Angstroms Resolution ;

Dokl.Biochem.(Engl.Transl.) (1974)

Cell Parameters of Crystalline Plant (Lupinus Luteus (Lupine)) Hemoglobin (Russian)

Kristallografiya (1971)

Unit-Cell Parameters of Crystalline Plant Hemoglobin

Sov.Phys.Crystallogr.(Engl.Transl.) (1971)

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晶胞边长 a length_a	93.470 Å
晶胞边长 b length_b	51.980 Å
晶胞边长 c length_c	38.320 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.80 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.1750
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/gd/1gdl/1gdl.fit
pddf	/app/data/pr_computation/gd/1gdl/1gdl.pr.out
profile	/app/data/saxs_computation/gd/1gdl/1gdl.dat