SAXSdb — 2flh

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2flh
沉积日期 deposition_date	2006-01-06
结构标题 title	Crystal structure of cytokinin-specific binding protein from mung bean in complex with cytokinin
关键词 keywords	cytokinins, zeatin, pathogenesis-related proteins, multiple-ligand binding, PLANT PROTEIN; PLANT PROTEIN
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	34.68 Å
回转半径 Rg (电子) rg_electron	34.82 Å
零角强度 I(0) i0	73405900.00
分子量 molecular_weight	70514.0 kDa
排除体积 excluded_volume	89189 Å³
包络体积 envelope_volume	111590 Å³
水化壳体积 shell_volume	29801 Å³
包络直径 envelope_diameter	132.2 Å
壳层 Rg shell_rg	36.74 Å
包络 Rg envelope_rg	34.77 Å
形状 Rg shape_rg	34.81 Å
总 Rg total_rg	35.02 Å
总原子数 total_atoms	4983
残基数 n_residues	602
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	126.5 Å
Rg (实空间) rg_real	35.16 Å
Rg 误差 (实空间) rg_real_error	1.55 Å
I(0) (实空间) i0_real	7.3410e+07
I(0) 误差 (实空间) i0_real_error	1.4040e+06
Rg (倒空间) rg_reciprocal	34.86 Å
I(0) (倒空间) i0_reciprocal	73390000.0000
解质量估计 total_estimate	0.7502
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	27.5 Å
偏度 Skewness skewness	0.634
峰度 Kurtosis kurtosis	-0.252
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	23260000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.477; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.446; Smooth: 0.870

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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	cytokinin-specific binding protein
分子量 formula_weight	17612.9 kDa
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	5855

MVKEFNTQTELSVRLEALWAVLSKDFITVVPKVLPHIVKDVQLIEGDGGVGTILIFNFLPEVSPSYQREEITEFDESSHEIGLQVIEGGYLSQGLSYYKTTFKLSEIEEDKTLVNVKISYDHDSDIEEKVTPTKTSQSTLMYLRRLERYLSNGSA

来源 Source

来源生物 organism	Vigna radiata
NCBI 分类编号 ncbi_taxonomy_id	157791
宿主生物 host_organism	Escherichia coli BL21

Entity 2 non-polymer

描述 description	(2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol
分子量 formula_weight	219.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	9

Entity 3 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	645

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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	d2flha_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.3 — Bet v1-like
家族 Family family	d.129.3.0 — automated matches

结构域编号 domain_id	d2flhb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.3 — Bet v1-like
家族 Family family	d.129.3.0 — automated matches

结构域编号 domain_id	d2flhc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.3 — Bet v1-like
家族 Family family	d.129.3.0 — automated matches

结构域编号 domain_id	d2flhd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.3 — Bet v1-like
家族 Family family	d.129.3.0 — automated matches

CATH v4.4 (4 domains)

结构域编号 domain_id	2flhA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	530 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	20 — START domain

结构域编号 domain_id	2flhB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	530 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	20 — START domain

结构域编号 domain_id	2flhC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	530 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	20 — START domain

结构域编号 domain_id	2flhD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	530 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	20 — START domain

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7. 引用文献 (6)

Crystal Structure of Vigna radiata Cytokinin-Specific Binding Protein in Complex with Zeatin.

Plant Cell (2006)

PMID: 16998071 · DOI: 10.1105/tpc.105.037119 PRIMARY

Structure of a yellow lupine pathogenesis-related PR-10 protein belonging to a novel subclass

Acta Crystallogr.,Sect.D (2005)

PMID: 15608381 · DOI: 10.1107/S0907444904028173

Crystallization and preliminary crystallographic studies of mung bean cytokinin-specific binding protein

Acta Crystallogr.,Sect.D (2003)

PMID: 12595714 · DOI: 10.1107/S0907444902022916

Crystal structures of two homologous pathogenesis-related proteins from yellow lupine

J.Mol.Biol. (2002)

PMID: 12079359 · DOI: 10.1016/S0022-2836(02)00385-6

Purification and cDNA cloning of cytokinin-specific binding protein from mung bean (Vigna radiata)

Eur.J.Biochem. (1998)

PMID: 9874249 · DOI: 10.1046/j.1432-1327.1998.2580794.x

X-ray and NMR structure of Bet v 1, the origin of birch pollen allergy.

Nat.Struct.Biol. (1996)

PMID: 8946858 · DOI: 10.1038/nsb1296-1040

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晶胞边长 a length_a	113.790 Å
晶胞边长 b length_b	113.790 Å
晶胞边长 c length_c	86.980 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	24

空间群 space_group	P 64
空间群编号 int_tables_number	172
晶系 crystal_system	—

分辨率 resolution	1.200 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.1570
R_work r_work	—
R_free r_free	0.1900

fit	/app/data/saxs_computation/fl/2flh/2flh.fit
pddf	/app/data/pr_computation/fl/2flh/2flh.pr.out
profile	/app/data/saxs_computation/fl/2flh/2flh.dat

Crystal structure of cytokinin-specific binding protein from mung bean in complex with cytokinin

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