SAXSdb — 1hy0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hy0
沉积日期 deposition_date	2001-01-17
结构标题 title	CRYSTAL STRUCTURE OF WILD TYPE DUCK DELTA 1 CRYSTALLIN (EYE LENS PROTEIN)
关键词 keywords	EYE LENS PROTEIN, DELTA 1 CRYSTALLIN, ARGININOSUCCINATE LYASE, 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	35.04 Å
回转半径 Rg (电子) rg_electron	34.39 Å
零角强度 I(0) i0	144387000.00
分子量 molecular_weight	98684.0 kDa
排除体积 excluded_volume	124870 Å³
包络体积 envelope_volume	161360 Å³
水化壳体积 shell_volume	39342 Å³
包络直径 envelope_diameter	110.7 Å
壳层 Rg shell_rg	40.68 Å
包络 Rg envelope_rg	33.75 Å
形状 Rg shape_rg	34.38 Å
总 Rg total_rg	34.92 Å
总原子数 total_atoms	6922
残基数 n_residues	895
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	108.7 Å
Rg (实空间) rg_real	34.90 Å
Rg 误差 (实空间) rg_real_error	0.81 Å
I(0) (实空间) i0_real	1.4440e+08
I(0) 误差 (实空间) i0_real_error	2.1710e+06
Rg (倒空间) rg_reciprocal	34.99 Å
I(0) (倒空间) i0_reciprocal	144400000.0000
解质量估计 total_estimate	0.9096
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	50.7 Å
偏度 Skewness skewness	0.053
峰度 Kurtosis kurtosis	-0.718
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	18890000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.955

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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	DELTA CRYSTALLIN I
分子量 formula_weight	51210.9 kDa
EC 编号 ec_number	4.3.2.1
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	7438

MASEGDKLMGGRFVGSTDPIMQMLSTSISTEQRLSEVDIQASIAYAKALEKAGILTKTELEKILSGLEKISEELSKGVIVVTQSDEDIQTANERRLKELIGDIAGKLHTGRSRNEQVVTDLKLFMKNSLSIISTHLLQLIKTLVERAAIEIDVILPGYTHLQKAQPIRWSQFLLSHAVALTRDSERLGEVKKRINVLPLGSGALAGNPLDIDREMLRSELEFASISLNSMDAISERDFVVEFLSVATLLLIHLSKMAEDLIIYSTSEFGFLTLSDAFSTGSSLMPQKKNPDSLELIRSKSGRVFGRLASILMVLKGLPSTYNKDLQEDKEAVIDVVDTLTAVLQVATGVISTLQISKENMEKALTPEMLATDLALYLVRKGMPFRQAHTASGKAVHLAETKGIAINNLTLEDLKSISPLFSSDVSQVFNFVNSVEQYTALGGTAKSSVTTQIEQLRELMKKQKEQA

来源 Source

来源生物 organism	Anas platyrhynchos
NCBI 分类编号 ncbi_taxonomy_id	8839
宿主生物 host_organism	Escherichia coli BL21

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	516

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1hy0a_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.127 — L-aspartase-like
超家族 Superfamily superfamily	a.127.1 — L-aspartase-like
家族 Family family	a.127.1.1 — L-aspartase/fumarase

结构域编号 domain_id	d1hy0b_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.127 — L-aspartase-like
超家族 Superfamily superfamily	a.127.1 — L-aspartase-like
家族 Family family	a.127.1.1 — L-aspartase/fumarase

CATH v4.4 (6 domains)

结构域编号 domain_id	1hy0A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	275 — Fumarase C; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

结构域编号 domain_id	1hy0A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	200 — Fumarase C; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

结构域编号 domain_id	1hy0A03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
同源超家族 H-superfamily homologous superfamily	30 — Fumarase/aspartase (C-terminal domain)

结构域编号 domain_id	1hy0B01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	275 — Fumarase C; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

结构域编号 domain_id	1hy0B02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	200 — Fumarase C; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

结构域编号 domain_id	1hy0B03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
同源超家族 H-superfamily homologous superfamily	30 — Fumarase/aspartase (C-terminal domain)

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7. 引用文献 (1)

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晶胞边长 a length_a	100.600 Å
晶胞边长 b length_b	100.600 Å
晶胞边长 c length_c	168.000 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	19.990 Å
R 因子 r_factor	0.2070
R_work r_work	0.1900
R_free r_free	0.2330

fit	/app/data/saxs_computation/hy/1hy0/1hy0.fit
pddf	/app/data/pr_computation/hy/1hy0/1hy0.pr.out
profile	/app/data/saxs_computation/hy/1hy0/1hy0.dat

CRYSTAL STRUCTURE OF WILD TYPE DUCK DELTA 1 CRYSTALLIN (EYE LENS PROTEIN)

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