SAXSdb — 1lrh

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1lrh
沉积日期 deposition_date	2002-05-15
结构标题 title	Crystal structure of auxin-binding protein 1 in complex with 1-naphthalene acetic acid
关键词 keywords	BETA JELLYROLL, DOUBLE STRANDED PARALLEL BETA HELIX, GERMIN LIKE PROTEIN, PROTEIN BINDING; PROTEIN BINDING
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	32.84 Å
回转半径 Rg (电子) rg_electron	32.53 Å
零角强度 I(0) i0	94214800.00
分子量 molecular_weight	77244.0 kDa
排除体积 excluded_volume	96484 Å³
包络体积 envelope_volume	122020 Å³
水化壳体积 shell_volume	32776 Å³
包络直径 envelope_diameter	112.6 Å
壳层 Rg shell_rg	37.71 Å
包络 Rg envelope_rg	32.06 Å
形状 Rg shape_rg	32.54 Å
总 Rg total_rg	32.94 Å
总原子数 total_atoms	5424
残基数 n_residues	640
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	107.5 Å
Rg (实空间) rg_real	33.10 Å
Rg 误差 (实空间) rg_real_error	0.97 Å
I(0) (实空间) i0_real	9.4210e+07
I(0) 误差 (实空间) i0_real_error	1.6800e+06
Rg (倒空间) rg_reciprocal	33.00 Å
I(0) (倒空间) i0_reciprocal	94210000.0000
解质量估计 total_estimate	0.8519
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	29.1 Å
偏度 Skewness skewness	0.429
峰度 Kurtosis kurtosis	-0.583
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12990000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.838; Smooth: 0.792

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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	auxin-binding protein 1
分子量 formula_weight	18411.8 kDa
突变 mutation	D161E/E162Q
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	5799

SCVRDNSLVRDISQMPQSSYGIEGLSHITVAGALNHGMKEVEVWLQTISPGQRTPIHRHSCEEVFTVLKGKGTLLMGSSSLKYPGQPQEIPFFQNTTFSIPVNDPHQVWNSDEHEDLQVLVIISRPPAKIFLYDDWSMPHTAAVLKFPFVWDEDCFEAAKEQL

来源 Source

来源生物 organism	Zea mays
NCBI 分类编号 ncbi_taxonomy_id	4577
宿主生物 host_organism	Trichoplusia ni

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1073.0 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	NAPHTHALEN-1-YL-ACETIC ACID
分子量 formula_weight	186.2 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	375

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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	d1lrha_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.1 — RmlC-like cupins
家族 Family family	b.82.1.2 — Germin/Seed storage 7S protein

结构域编号 domain_id	d1lrhb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.1 — RmlC-like cupins
家族 Family family	b.82.1.2 — Germin/Seed storage 7S protein

结构域编号 domain_id	d1lrhc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.1 — RmlC-like cupins
家族 Family family	b.82.1.2 — Germin/Seed storage 7S protein

结构域编号 domain_id	d1lrhd_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.1 — RmlC-like cupins
家族 Family family	b.82.1.2 — Germin/Seed storage 7S protein

CATH v4.4 (4 domains)

结构域编号 domain_id	1lrhA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	10 — Jelly Rolls

结构域编号 domain_id	1lrhB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	10 — Jelly Rolls

结构域编号 domain_id	1lrhC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	10 — Jelly Rolls

结构域编号 domain_id	1lrhD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	10 — Jelly Rolls

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7. 引用文献 (1)

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晶胞边长 a length_a	61.583 Å
晶胞边长 b length_b	82.433 Å
晶胞边长 c length_c	69.962 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.37 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2400

fit	/app/data/saxs_computation/lr/1lrh/1lrh.fit
pddf	/app/data/pr_computation/lr/1lrh/1lrh.pr.out
profile	/app/data/saxs_computation/lr/1lrh/1lrh.dat

Crystal structure of auxin-binding protein 1 in complex with 1-naphthalene acetic acid

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

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 branched

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)