1gbf

;ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA AND GLY 216 REPLACED BY LEU COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACID ;

Method: X-RAY DIFFRACTION D_max: 51.6 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gbf
沉积日期 deposition_date	1995-09-06
结构标题 title	;ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA AND GLY 216 REPLACED BY LEU COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACID ;
关键词 keywords	ACTIVE-SITE MUTATION, SERINE PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	16.20 Å
回转半径 Rg (电子) rg_electron	15.03 Å
零角强度 I(0) i0	8821720.00
分子量 molecular_weight	20386.0 kDa
排除体积 excluded_volume	24891 Å³
包络体积 envelope_volume	27101 Å³
水化壳体积 shell_volume	14920 Å³
包络直径 envelope_diameter	51.2 Å
壳层 Rg shell_rg	21.28 Å
包络 Rg envelope_rg	15.31 Å
形状 Rg shape_rg	15.00 Å
总 Rg total_rg	16.11 Å
总原子数 total_atoms	1425
残基数 n_residues	201
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	51.6 Å
Rg (实空间) rg_real	16.07 Å
Rg 误差 (实空间) rg_real_error	0.23 Å
I(0) (实空间) i0_real	8.8220e+06
I(0) 误差 (实空间) i0_real_error	1.0330e+05
Rg (倒空间) rg_reciprocal	16.08 Å
I(0) (倒空间) i0_reciprocal	8822000.0000
解质量估计 total_estimate	0.8863
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	50.3 Å
偏度 Skewness skewness	0.096
峰度 Kurtosis kurtosis	-0.433
角度范围 angular_range	— – 0.4900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2701000.0000
实空间数据点数 n_real_points	79
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.997

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	ALPHA-LYTIC PROTEASE
分子量 formula_weight	19871.1 kDa
EC 编号 ec_number	3.4.21.12
突变 mutation	M190A, G216L
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	1595

ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACAGRGDSGGSWITSAGQAQGVMSGLNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG

来源 Source

来源生物 organism	Lysobacter enzymogenes
NCBI 分类编号 ncbi_taxonomy_id	69
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACID INHIBITOR
分子量 formula_weight	442.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

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

XAAPA

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	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	170

▼

6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1gbfa_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.47 — Trypsin-like serine proteases
超家族 Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
家族 Family family	b.47.1.1 — Prokaryotic proteases

CATH v4.4 (2 domains)

结构域编号 domain_id	1gbfA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

结构域编号 domain_id	1gbfA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

▶

7. 引用文献 (7)

;Kinetic and structural characterization of mutations of glycine 216 in alpha-lytic protease: a new target for engineering substrate specificity. ;

J.Mol.Biol. (1995)

PMID: 7500345 · DOI: 10.1006/jmbi.1995.0650 PRIMARY

Structural Basis for Broad Specificity in Alpha-Lytic Protease

Biochemistry (1991)

Structural Plasticity Broadens the Specificity of an Engineered Protease

Nature (1989)

Structural Analysis of Specificity: Alpha-Lytic Protease Complexes with Analogues of Reaction Intermediates

Biochemistry (1989)

Serine Protease Mechanism: Structure of an Inhibitory Complex of Alpha-Lytic Protease and a Tightly Bound Peptide Boronic Acid

Biochemistry (1987)

Refined Structure of Alpha-Lytic Protease at 1.7 Angstroms Resolution. Analysis of Hydrogen Bonding and Solvent Structure

J.Mol.Biol. (1985)

Molecular Structure of the Alpha-Lytic Protease from Myxobacter 495 at 2.8 Angstroms Resolution

J.Mol.Biol. (1979)

▶

晶胞边长 a length_a	66.200 Å
晶胞边长 b length_b	66.200 Å
晶胞边长 c length_c	80.180 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	6

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	—

分辨率 resolution	2.150 Å
最低分辨率 resolution_low	17.500 Å
R 因子 r_factor	0.1400
R_work r_work	0.1400
R_free r_free	—

fit	/app/data/saxs_computation/gb/1gbf/1gbf.fit
pddf	/app/data/pr_computation/gb/1gbf/1gbf.pr.out
profile	/app/data/saxs_computation/gb/1gbf/1gbf.dat

;ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA AND GLY 216 REPLACED BY LEU COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC 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

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. 引用文献 (7)

8. 文件与曲线 (10)

Files (7)

Curves (3)