SAXSdb — 2bqa

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2bqa
沉积日期 deposition_date	1998-05-21
结构标题 title	CONTRIBUTION OF HYDROPHOBIC EFFECT TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME
关键词 keywords	ENZYME, HYDROLASE, O-GLYCOSYL, ALPHA, BETA, GLYCOSIDASE; HYDROLASE
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	15.51 Å
回转半径 Rg (电子) rg_electron	14.16 Å
零角强度 I(0) i0	4739200.00
分子量 molecular_weight	14668.0 kDa
排除体积 excluded_volume	17974 Å³
包络体积 envelope_volume	20293 Å³
水化壳体积 shell_volume	12274 Å³
包络直径 envelope_diameter	50.3 Å
壳层 Rg shell_rg	19.80 Å
包络 Rg envelope_rg	14.46 Å
形状 Rg shape_rg	14.13 Å
总 Rg total_rg	15.31 Å
总原子数 total_atoms	1028
残基数 n_residues	130
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	51.3 Å
Rg (实空间) rg_real	15.43 Å
Rg 误差 (实空间) rg_real_error	0.26 Å
I(0) (实空间) i0_real	4.7390e+06
I(0) 误差 (实空间) i0_real_error	5.1620e+04
Rg (倒空间) rg_reciprocal	15.44 Å
I(0) (倒空间) i0_reciprocal	4739000.0000
解质量估计 total_estimate	0.8802
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	20.8 Å
偏度 Skewness skewness	0.184
峰度 Kurtosis kurtosis	-0.290
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	809400.0000
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: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.994

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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 (3)

Entity 1 polymer

描述 description	LYSOZYME
分子量 formula_weight	14656.6 kDa
EC 编号 ec_number	3.2.1.17
突变 mutation	C77A, C95A
来源方法 src_method	man
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	1183

KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAVAAAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 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	1

Entity 3 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	155

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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	d2bqaa_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.2 — Lysozyme-like
超家族 Superfamily superfamily	d.2.1 — Lysozyme-like
家族 Family family	d.2.1.2 — C-type lysozyme

CATH v4.4 (1 domains)

结构域编号 domain_id	2bqaA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	530 — Lysozyme
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (8)

;A general rule for the relationship between hydrophobic effect and conformational stability of a protein: stability and structure of a series of hydrophobic mutants of human lysozyme. ;

J.Mol.Biol. (1998)

PMID: 9677301 · DOI: 10.1006/jmbi.1998.1906 PRIMARY

;Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme: Calorimetry and X-Ray Analysis of Six Tyrosine--> Phenylalanine Mutants ;

Biochemistry (1998)

;Contribution of the Hydrophobic Effect to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analyses of the Nine Valine to Alanine Mutants ;

Biochemistry (1997)

Contribution of Water Molecules in the Interior of a Protein to the Conformational Stability

J.Mol.Biol. (1997)

The Structure, Stability, and Folding Process of Amyloidogenic Mutant Human Lysozyme

J.Biochem.(Tokyo) (1996)

;Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants ;

J.Mol.Biol. (1995)

Enthalpic Destabilization of a Mutant Human Lysozyme Lacking a Disulfide Bridge between Cysteine-77 and Cysteine-95

Biochemistry (1992)

The Crystal Structure of a Mutant Human Lysozyme C77/95A with Increased Secretion Efficiency in Yeast

J.Biol.Chem. (1991)

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晶胞边长 a length_a	56.930 Å
晶胞边长 b length_b	60.910 Å
晶胞边长 c length_c	33.570 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	4

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	1.800 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.1700
R_work r_work	0.1700
R_free r_free	—

fit	/app/data/saxs_computation/bq/2bqa/2bqa.fit
pddf	/app/data/pr_computation/bq/2bqa/2bqa.pr.out
profile	/app/data/saxs_computation/bq/2bqa/2bqa.dat

CONTRIBUTION OF HYDROPHOBIC EFFECT TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME

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