1gdj

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

Method: X-RAY DIFFRACTION D_max: 50.9 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	1gdj
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	16.42 Å
回转半径 Rg (电子) rg_electron	14.86 Å
零角强度 I(0) i0	5069120.00
分子量 molecular_weight	17249.0 kDa
排除体积 excluded_volume	22022 Å³
包络体积 envelope_volume	24037 Å³
水化壳体积 shell_volume	13684 Å³
包络直径 envelope_diameter	50.3 Å
壳层 Rg shell_rg	20.75 Å
包络 Rg envelope_rg	15.08 Å
形状 Rg shape_rg	14.83 Å
总 Rg total_rg	16.12 Å
总原子数 total_atoms	1220
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	50.9 Å
Rg (实空间) rg_real	16.31 Å
Rg 误差 (实空间) rg_real_error	0.28 Å
I(0) (实空间) i0_real	5.0690e+06
I(0) 误差 (实空间) i0_real_error	5.4920e+04
Rg (倒空间) rg_reciprocal	16.32 Å
I(0) (倒空间) i0_reciprocal	5069000.0000
解质量估计 total_estimate	0.8974
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	22.2 Å
偏度 Skewness skewness	0.096
峰度 Kurtosis kurtosis	-0.476
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	1189000.0000
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: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.973

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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 (3)

Entity 1 polymer

描述 description	LEGHEMOGLOBIN (DEOXY)
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	1470

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 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	243

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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	d1gdja_
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	1gdjA00
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 (21)

The Structure of Deoxy- and Oxy-Leghaemoglobin from Lupin

J.Mol.Biol. (1995)

PMID: 7643380 · DOI: 10.1006/jmbi.1995.0419 PRIMARY

Crystal Structure of Ferric Complexes of the Yellow Lupin Leghemoglobin with Isoquinoline at 1.8 Angstroms Resolution (Russian)

Bioorg.Khim. (1991)

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)

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

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

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)

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	93.480 Å
晶胞边长 b length_b	51.600 Å
晶胞边长 c length_c	38.330 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	1.700 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.1650
R_work r_work	—
R_free r_free	—

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