SAXSdb — 1t8n

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1t8n
沉积日期 deposition_date	2004-05-13
结构标题 title	CRYSTAL STRUCTURE OF THE P1 THR BPTI MUTANT- BOVINE CHYMOTRYPSIN COMPLEX
关键词 keywords	;CHYMOTRYPSIN, SERINE PROTEINASE, BOVINE PANCREATIC TRYPSIN INHIBITOR, BPTI, PROTEIN-PROTEIN INTERACTION, NON-COGNATE BINDING, S1 POCKET, PRIMARY SPECIFICITY, HYDROLASE-HYDROLASE INHIBITOR COMPLEX ;; HYDROLASE/HYDROLASE INHIBITOR
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	29.79 Å
回转半径 Rg (电子) rg_electron	29.75 Å
零角强度 I(0) i0	70472700.00
分子量 molecular_weight	63804.0 kDa
排除体积 excluded_volume	78878 Å³
包络体积 envelope_volume	96557 Å³
水化壳体积 shell_volume	28446 Å³
包络直径 envelope_diameter	102.7 Å
壳层 Rg shell_rg	35.29 Å
包络 Rg envelope_rg	29.53 Å
形状 Rg shape_rg	29.74 Å
总 Rg total_rg	30.28 Å
总原子数 total_atoms	4454
残基数 n_residues	594
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	96.1 Å
Rg (实空间) rg_real	30.01 Å
Rg 误差 (实空间) rg_real_error	0.80 Å
I(0) (实空间) i0_real	7.0470e+07
I(0) 误差 (实空间) i0_real_error	1.1760e+06
Rg (倒空间) rg_reciprocal	29.92 Å
I(0) (倒空间) i0_reciprocal	70470000.0000
解质量估计 total_estimate	0.6100
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	27.2 Å
偏度 Skewness skewness	0.458
峰度 Kurtosis kurtosis	-0.618
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	24410000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.741; Stabil: 1.000; Sysdev: 0.050; Positv: 1.000; Valcen: 0.811; Smooth: 0.740

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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	Chymotrypsin A
分子量 formula_weight	25686.0 kDa
EC 编号 ec_number	3.4.21.1
突变 mutation	K50T, M87L
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	A,C
原子数 atom_count	5032

CGVPAIQPVLSGLSRIVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTTCVTTGWGLTRYTNANTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN

Entity 2 polymer

描述 description	Pancreatic trypsin inhibitor
分子量 formula_weight	6481.5 kDa
来源方法 src_method	man
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

RPDFCLEPPYTGPCTARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCLRTCGGA

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI 分类编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	8

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	520

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1t8na_
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.47.1.2 — Eukaryotic proteases

结构域编号 domain_id	d1t8nb_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.8 — BPTI-like
超家族 Superfamily superfamily	g.8.1 — BPTI-like
家族 Family family	g.8.1.1 — Small Kunitz-type inhibitors & BPTI-like toxins

结构域编号 domain_id	d1t8nc_
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.47.1.2 — Eukaryotic proteases

结构域编号 domain_id	d1t8nd_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.8 — BPTI-like
超家族 Superfamily superfamily	g.8.1 — BPTI-like
家族 Family family	g.8.1.1 — Small Kunitz-type inhibitors & BPTI-like toxins

CATH v4.4 (6 domains)

结构域编号 domain_id	1t8nA01
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	1t8nA02
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	1t8nB00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	410 — Factor Xa Inhibitor
同源超家族 H-superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

结构域编号 domain_id	1t8nC01
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	1t8nC02
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	1t8nD00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	410 — Factor Xa Inhibitor
同源超家族 H-superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

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7. 引用文献 (7)

Crystal structures of five bovine chymotrypsin complexes with P1 BPTI variants.

J.Mol.Biol. (2004)

PMID: 15544809 · DOI: 10.1016/j.jmb.2004.09.088 PRIMARY

;STRUCTURAL CONSEQUENCES OF ACCOMMODATION OF FOUR NON-COGNATE AMINO-ACID RESIDUES IN THE S1 POCKET OF BOVINE TRYPSIN AND CHYMOTRYPSIN ;

J.Mol.Biol. (2003)

DOI: 10.1016/j.jmb.2003.08.059

ULTRAHIGH-RESOLUTION STRUCTURE OF A BPTI MUTANT

Acta Crystallogr.,Sect.D (2001)

DOI: 10.1107/S0907444901003468

;Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): engineering of inhibitors with altered specificities ;

Protein Sci. (1997)

;Crystal structure of the bovine alpha-chymotrypsin:Kunitz inhibitor complex. An example of multiple protein:protein recognition sites. ;

J.Mol.Recog. (1997)

DOI: 10.1002/(SICI)1099-1352(199701/02)10:1<26::AID-JMR351>3.0.CO;2-N

CRYSTALLOGRAPHIC REFINEMENT OF THE STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR AT 1.5 A RESOLUTION

Acta Crystallogr.,Sect.B (1975)

DOI: 10.1107/S0567740875002415

Three-dimensional structure of tosyl-alpha-chymotrypsin

Nature (1967)

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晶胞边长 a length_a	99.960 Å
晶胞边长 b length_b	99.960 Å
晶胞边长 c length_c	205.360 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	12

空间群 space_group	P 61
空间群编号 int_tables_number	169
晶系 crystal_system	—

分辨率 resolution	1.750 Å
最低分辨率 resolution_low	14.980 Å
R 因子 r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2140

fit	/app/data/saxs_computation/t8/1t8n/1t8n.fit
pddf	/app/data/pr_computation/t8/1t8n/1t8n.pr.out
profile	/app/data/saxs_computation/t8/1t8n/1t8n.dat

CRYSTAL STRUCTURE OF THE P1 THR BPTI MUTANT- BOVINE CHYMOTRYPSIN COMPLEX

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

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. 引用文献 (7)

8. 文件与曲线 (10)

Files (7)

Curves (3)