SAXSdb — 1k75

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1k75
沉积日期 deposition_date	2001-10-18
结构标题 title	The L-histidinol dehydrogenase (hisD) structure implicates domain swapping and gene duplication.
关键词 keywords	;L-histidinol dehydrogenase, homodimer, Rossmann fold, 4 domains, hisD, L-histidine biosynthesis, NAD cofactor, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, Structural Genomics, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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	29.53 Å
回转半径 Rg (电子) rg_electron	28.54 Å
零角强度 I(0) i0	145264000.00
分子量 molecular_weight	92517.0 kDa
排除体积 excluded_volume	114610 Å³
包络体积 envelope_volume	138780 Å³
水化壳体积 shell_volume	39830 Å³
包络直径 envelope_diameter	97.4 Å
壳层 Rg shell_rg	36.59 Å
包络 Rg envelope_rg	28.52 Å
形状 Rg shape_rg	28.55 Å
总 Rg total_rg	29.24 Å
总原子数 total_atoms	6446
残基数 n_residues	850
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	91.6 Å
Rg (实空间) rg_real	29.44 Å
Rg 误差 (实空间) rg_real_error	0.51 Å
I(0) (实空间) i0_real	1.4530e+08
I(0) 误差 (实空间) i0_real_error	2.0010e+06
Rg (倒空间) rg_reciprocal	29.48 Å
I(0) (倒空间) i0_reciprocal	145300000.0000
解质量估计 total_estimate	0.9041
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	33.9 Å
偏度 Skewness skewness	0.252
峰度 Kurtosis kurtosis	-0.443
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	46620000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.928

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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	L-histidinol dehydrogenase
分子量 formula_weight	46434.5 kDa
EC 编号 ec_number	1.1.1.23
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	7382

MSFNTIIDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKVSAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQDVFNVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVLVIADSGATPDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQALNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKNAVTLRVNALKEQA

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

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	4

Entity 3 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 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	924

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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	d1k75a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.2 — L-histidinol dehydrogenase HisD

结构域编号 domain_id	d1k75b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.2 — L-histidinol dehydrogenase HisD

CATH v4.4 (6 domains)

结构域编号 domain_id	1k75A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1k75A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	1300 —

结构域编号 domain_id	1k75A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1k75B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1k75B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1k75B03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	1300 —

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7. 引用文献 (1)

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晶胞边长 a length_a	54.370 Å
晶胞边长 b length_b	107.520 Å
晶胞边长 c length_c	157.200 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	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.750 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	—
R_work r_work	0.1900
R_free r_free	0.2250

fit	/app/data/saxs_computation/k7/1k75/1k75.fit
pddf	/app/data/pr_computation/k7/1k75/1k75.pr.out
profile	/app/data/saxs_computation/k7/1k75/1k75.dat

The L-histidinol dehydrogenase (hisD) structure implicates domain swapping and gene duplication.

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