SAXSdb — 2izk

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2izk
沉积日期 deposition_date	1997-08-13
结构标题 title	STREPTAVIDIN-GLYCOLURIL PH 2.58 I4122 COMPLEX
关键词 keywords	BIOTIN-BINDING PROTEIN, STREPTAVIDIN-SMALL MOLECULE LIGAND, DESIGNED SMALL MOLECULE LIGAND WITH MICROMOLAR AFFINITY; BIOTIN-BINDING 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	15.95 Å
回转半径 Rg (电子) rg_electron	14.95 Å
零角强度 I(0) i0	3872980.00
分子量 molecular_weight	13251.0 kDa
排除体积 excluded_volume	16223 Å³
包络体积 envelope_volume	18962 Å³
水化壳体积 shell_volume	11307 Å³
包络直径 envelope_diameter	55.4 Å
壳层 Rg shell_rg	20.00 Å
包络 Rg envelope_rg	15.69 Å
形状 Rg shape_rg	14.91 Å
总 Rg total_rg	16.00 Å
总原子数 total_atoms	1810
残基数 n_residues	123
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	55.0 Å
Rg (实空间) rg_real	15.98 Å
Rg 误差 (实空间) rg_real_error	0.34 Å
I(0) (实空间) i0_real	3.8730e+06
I(0) 误差 (实空间) i0_real_error	4.3720e+04
Rg (倒空间) rg_reciprocal	15.98 Å
I(0) (倒空间) i0_reciprocal	3873000.0000
解质量估计 total_estimate	0.7903
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	18.1 Å
偏度 Skewness skewness	0.418
峰度 Kurtosis kurtosis	-0.158
角度范围 angular_range	— – 0.5000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	606400.0000
实空间数据点数 n_real_points	80
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.928; Smooth: 0.000

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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	STREPTAVIDIN
分子量 formula_weight	12965.0 kDa
来源方法 src_method	nat
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	2233

AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP

Entity 2 non-polymer

描述 description	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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	1

Entity 4 non-polymer

描述 description	GLYCOLURIL
分子量 formula_weight	142.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	74

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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	d2izka_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.61 — Streptavidin-like
超家族 Superfamily superfamily	b.61.1 — Avidin/streptavidin
家族 Family family	b.61.1.1 — Avidin/streptavidin

CATH v4.4 (1 domains)

结构域编号 domain_id	2izkA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	128 — Lipocalin
同源超家族 H-superfamily homologous superfamily	30 — Avidin-like

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7. 引用文献 (7)

Binding of biotin to streptavidin stabilizes intersubunit salt bridges between Asp61 and His87 at low pH.

J.Mol.Biol. (1997)

PMID: 9405158 · DOI: 10.1006/jmbi.1997.1444 PRIMARY

;In Crystals of Complexes of Streptavidin with Peptide Ligands Containing the Hpq Sequence the Pka of the Peptide Histidine is Less Than 3.0 ;

J.Biol.Chem. (1997)

;Structure-Based Design Tools: Structural and Thermodynamic Comparison with Biotin of a Small Molecule that Binds Streptavidin with Micromolar Affinity ;

J.Am.Chem.Soc. (1996)

Preparation of a Protein-Dimerizing Ligand by Topochemistry and Structure-Based Design

J.Am.Chem.Soc. (1996)

Topochemical Catalysis Achieved by Structure-Based Design

J.Biol.Chem. (1995)

;Binding to Protein Targets of Peptidic Leads Discovered by Phage Display: Crystal Structures of Streptavidin-Bound Linear and Cyclic Peptide Ligands Containing the Hpq Sequence ;

Biochemistry (1995)

Structure-Based Design of High Affinity Streptavidin Binding Ligands Containing Thioether Crosslinks

J.Am.Chem.Soc. (1995)

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晶胞边长 a length_a	58.040 Å
晶胞边长 b length_b	58.040 Å
晶胞边长 c length_c	174.600 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	16

空间群 space_group	I 41 2 2
空间群编号 int_tables_number	98
晶系 crystal_system	—

分辨率 resolution	1.300 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	0.1780
R_work r_work	0.1780
R_free r_free	0.2020

fit	/app/data/saxs_computation/iz/2izk/2izk.fit
pddf	/app/data/pr_computation/iz/2izk/2izk.pr.out
profile	/app/data/saxs_computation/iz/2izk/2izk.dat

STREPTAVIDIN-GLYCOLURIL PH 2.58 I4122 COMPLEX

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution