SAXSdb — 1vwk

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1vwk
沉积日期 deposition_date	1997-03-03
结构标题 title	STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2
关键词 keywords	;COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE), LINEAR THIOETHER-CONTAINING PEPTIDE ENGINEERED, COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) complex ;; COMPLEX (BIOTIN-BINDING PROTEIN/PEPTIDE)
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	18.69 Å
回转半径 Rg (电子) rg_electron	17.64 Å
零角强度 I(0) i0	14606900.00
分子量 molecular_weight	27561.0 kDa
排除体积 excluded_volume	34000 Å³
包络体积 envelope_volume	39558 Å³
水化壳体积 shell_volume	18437 Å³
包络直径 envelope_diameter	67.2 Å
壳层 Rg shell_rg	24.20 Å
包络 Rg envelope_rg	18.21 Å
形状 Rg shape_rg	17.58 Å
总 Rg total_rg	18.78 Å
总原子数 total_atoms	3793
残基数 n_residues	260
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	61.9 Å
Rg (实空间) rg_real	18.59 Å
Rg 误差 (实空间) rg_real_error	0.43 Å
I(0) (实空间) i0_real	1.4610e+07
I(0) 误差 (实空间) i0_real_error	2.0050e+05
Rg (倒空间) rg_reciprocal	18.61 Å
I(0) (倒空间) i0_reciprocal	14610000.0000
解质量估计 total_estimate	0.8010
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	22.9 Å
偏度 Skewness skewness	0.198
峰度 Kurtosis kurtosis	-0.378
角度范围 angular_range	— – 0.4250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3934000.0000
实空间数据点数 n_real_points	74
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.804; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; 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 (4)

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	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D
原子数 atom_count	4671

AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP

Entity 2 polymer

描述 description	PEPTIDE LIGAND CONTAINING HPQ
分子量 formula_weight	863.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	M,P

HPQGPPCKX

Entity 3 non-polymer

描述 description	PENTANOIC ACID
分子量 formula_weight	102.1 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	171

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1vwkb_
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

结构域编号 domain_id	d1vwkd_
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 (2 domains)

结构域编号 domain_id	1vwkB00
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

结构域编号 domain_id	1vwkD00
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)

;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)

PMID: 9148939 · DOI: 10.1074/jbc.272.20.13220 PRIMARY

;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 Ligand Design

J.Biol.Chem. (1995)

Topochemistry for Preparing Ligands that Dimerize Receptors

Chem.Biol. (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 Cyclic Peptide Ligands Containing Thioether Cross-Links

J.Am.Chem.Soc. (1995)

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晶胞边长 a length_a	95.010 Å
晶胞边长 b length_b	105.420 Å
晶胞边长 c length_c	47.970 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 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	1.450 Å
最低分辨率 resolution_low	7.500 Å
R 因子 r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2400

fit	/app/data/saxs_computation/vw/1vwk/1vwk.fit
pddf	/app/data/pr_computation/vw/1vwk/1vwk.pr.out
profile	/app/data/saxs_computation/vw/1vwk/1vwk.dat

STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2

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 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. 引用文献 (7)

8. 文件与曲线 (10)

Files (7)

Curves (3)