1pww

;Crystal structure of Anthrax Lethal Factor active site mutant protein complexed with an optimised peptide substrate in the presence of zinc. ;

Method: X-RAY DIFFRACTION D_max: 117.7 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1pww
沉积日期 deposition_date	2003-07-02
结构标题 title	;Crystal structure of Anthrax Lethal Factor active site mutant protein complexed with an optimised peptide substrate in the presence of zinc. ;
关键词 keywords	Anthrax Toxin, Lethal Factor (active site mutant), optimised peptide substrate, hydrolase; 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	38.11 Å
回转半径 Rg (电子) rg_electron	37.45 Å
零角强度 I(0) i0	434403000.00
分子量 molecular_weight	172600.0 kDa
排除体积 excluded_volume	217460 Å³
包络体积 envelope_volume	291200 Å³
水化壳体积 shell_volume	63493 Å³
包络直径 envelope_diameter	121.8 Å
壳层 Rg shell_rg	44.65 Å
包络 Rg envelope_rg	36.82 Å
形状 Rg shape_rg	37.46 Å
总 Rg total_rg	37.89 Å
总原子数 total_atoms	12185
残基数 n_residues	1482
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	117.7 Å
Rg (实空间) rg_real	37.87 Å
Rg 误差 (实空间) rg_real_error	0.89 Å
I(0) (实空间) i0_real	4.3440e+08
I(0) 误差 (实空间) i0_real_error	7.3980e+06
Rg (倒空间) rg_reciprocal	38.02 Å
I(0) (倒空间) i0_reciprocal	434500000.0000
解质量估计 total_estimate	0.8988
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	51.7 Å
偏度 Skewness skewness	0.113
峰度 Kurtosis kurtosis	-0.520
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	107700000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.896

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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	Lethal factor
分子量 formula_weight	90330.8 kDa
EC 编号 ec_number	3.4.24.-
突变 mutation	E687C
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	A,B
原子数 atom_count	12185

AGGHGDVGMHVKEKEKNKDENKRKDEERNKTQEEHLKEIMKHIVKIEVKGEEAVKKEAAEKLLEKVPSDVLEMYKAIGGKIYIVDGDITKHISLEALSEDKKKIKDIYGKDALLHEHYVYAKEGYEPVLVIQSSEDYVENTEKALNVYYEIGKILSRDILSKINQPYQKFLDVLNTIKNASDSDGQDLLFTNQLKEHPTDFSVEFLEQNSNEVQEVFAKAFAYYIEPQHRDVLQLYAPEAFNYMDKFNEQEINLSLEELKDQRMLSRYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSLSQEEKELLKRIQIDSSDFLSTEEKEFLKKLQIDIRDSLSEEEKELLNRIQVDSSNPLSEKEKEFLKKLKLDIQPYDINQRLQDTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLTATLGADLVDSTDNTKINRGIFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLSPDTRAGYLENGKLILQRNIGLEIKDVQIIKQSEKEYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFNVHNRYASNIVESAYLILNEWKNNIQSDLIKKVTNYLVDGNGRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSILLHGPSKGVELRNDSEGFIHCFGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNEAEFFAEAFRLMHSTDHAERLKVQKNAPKTFQFINDQIKFIINS

来源 Source

来源生物 organism	Bacillus anthracis
NCBI 分类编号 ncbi_taxonomy_id	1392
宿主生物 host_organism	Bacillus anthracis

Entity 2 polymer

描述 description	LF20
分子量 formula_weight	2354.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,D

MLARRKKVYPYPMEPTIAEG

Entity 3 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1pwwa1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
家族 Family family	d.92.1.14 — Anthrax toxin lethal factor, N- and C-terminal domains

结构域编号 domain_id	d1pwwa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
家族 Family family	d.92.1.14 — Anthrax toxin lethal factor, N- and C-terminal domains

结构域编号 domain_id	d1pwwa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.166 — ADP-ribosylation
超家族 Superfamily superfamily	d.166.1 — ADP-ribosylation
家族 Family family	d.166.1.1 — ADP-ribosylating toxins

结构域编号 domain_id	d1pwwb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
家族 Family family	d.92.1.14 — Anthrax toxin lethal factor, N- and C-terminal domains

结构域编号 domain_id	d1pwwb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
家族 Family family	d.92.1.14 — Anthrax toxin lethal factor, N- and C-terminal domains

结构域编号 domain_id	d1pwwb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.166 — ADP-ribosylation
超家族 Superfamily superfamily	d.166.1 — ADP-ribosylation
家族 Family family	d.166.1.1 — ADP-ribosylating toxins

CATH v4.4 (8 domains)

结构域编号 domain_id	1pwwA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	1pwwA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

结构域编号 domain_id	1pwwA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2030 — Anthrax toxin lethal factor, domain 3, chain A
同源超家族 H-superfamily homologous superfamily	10 — Anthrax toxin lethal factor, domain 3, chain A

结构域编号 domain_id	1pwwA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	1pwwB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	1pwwB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

结构域编号 domain_id	1pwwB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2030 — Anthrax toxin lethal factor, domain 3, chain A
同源超家族 H-superfamily homologous superfamily	10 — Anthrax toxin lethal factor, domain 3, chain A

结构域编号 domain_id	1pwwB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

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7. 引用文献 (1)

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晶胞边长 a length_a	96.700 Å
晶胞边长 b length_b	137.400 Å
晶胞边长 c length_c	98.300 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	22.690 Å
R 因子 r_factor	0.2380
R_work r_work	0.2380
R_free r_free	0.2880

fit	/app/data/saxs_computation/pw/1pww/1pww.fit
pddf	/app/data/pr_computation/pw/1pww/1pww.pr.out
profile	/app/data/saxs_computation/pw/1pww/1pww.dat

;Crystal structure of Anthrax Lethal Factor active site mutant protein complexed with an optimised peptide substrate in the presence of zinc. ;

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)