1z1w

;Crystal structures of the tricorn interacting facor F3 from Thermoplasma acidophilum, a zinc aminopeptidase in three different conformations ;

Method: X-RAY DIFFRACTION D_max: 92.1 Å Quality: EXCELLENT

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	1z1w
沉积日期 deposition_date	2005-03-07
结构标题 title	;Crystal structures of the tricorn interacting facor F3 from Thermoplasma acidophilum, a zinc aminopeptidase in three different conformations ;
关键词 keywords	zinc aminopeptidase, Gluzincins, superhelix, 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	29.47 Å
回转半径 Rg (电子) rg_electron	28.49 Å
零角强度 I(0) i0	126876000.00
分子量 molecular_weight	89521.0 kDa
排除体积 excluded_volume	112160 Å³
包络体积 envelope_volume	137270 Å³
水化壳体积 shell_volume	39528 Å³
包络直径 envelope_diameter	97.4 Å
壳层 Rg shell_rg	36.45 Å
包络 Rg envelope_rg	28.37 Å
形状 Rg shape_rg	28.48 Å
总 Rg total_rg	29.29 Å
总原子数 total_atoms	6301
残基数 n_residues	780
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	92.1 Å
Rg (实空间) rg_real	29.38 Å
Rg 误差 (实空间) rg_real_error	0.56 Å
I(0) (实空间) i0_real	1.2690e+08
I(0) 误差 (实空间) i0_real_error	1.8400e+06
Rg (倒空间) rg_reciprocal	29.42 Å
I(0) (倒空间) i0_reciprocal	126900000.0000
解质量估计 total_estimate	0.9031
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	35.8 Å
偏度 Skewness skewness	0.253
峰度 Kurtosis kurtosis	-0.407
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	33320000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.941

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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	Tricorn protease interacting factor F3
分子量 formula_weight	89492.7 kDa
EC 编号 ec_number	3.4.11.-
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	6654

MEVEKYDLTLDFDIQKRTFNGTETITADAGDIVLDAVGLQINWMKVNGRDTAFTYDGQTVRAPGDSQPQKIEISFAGKVSDSLSGIYYAGRENGMITTHFEATDARRMFPCVDHPAYKAVFAITVVIDKDYDAISNMPPKRIEVSERKVVEFQDTPRMSTYLLYVGIGKFRYEYEKYRDIDLILASLKDIRSKYPLDMARKSVEFYENYFGIPYALPKMHLISVPEFGAGAMENWGAITFREIYMDIAENSAVTVKRNSANVIAHEIAHQWFGDLVTMKWWNDLWLNESFATFMSYKTMDTLFPEWSFWGDFFVSRTSGALRSDSLKNTHPIEVDVRDPDEISQIFDEISYGKGASILRMIEDYAGYEEFRKGISKYLNDHKFGNAEGSDLWTAIEDVSGKPVKRVMEYWIKNPGYPVIKLKRNGRKITMYQTRFLLNGEEEGRWPVPVNIKKKDGVERILLEDEASIEADGLIKINADSAGFYRVLYDDATFSDVMGHYRDLSPLDRIGLVDDLFAFLLSGHIDPETYRQRIRNFFDDEDHNVITAIVGQMEYLRMLTHAFDDDARAFCRSRMQFLTGKQDENLKIALGRVSRLYVMVDESYAEEMSKLFKDFDSAEPEMRSSIATAYALVTGDLKGLLEKFRSVDRDEDRVRIISAFGKLKSNTDLSTVYGMVEKTEIKKQDMISFFSSALETLPGREFIFANLDRIIRLVIRYFTGNRTASRTVEMMIPVIGLDHPDAEDIVRNIGSKNISMGLAKGIEMLAVNRKLVERIRQTAVK

来源 Source

来源生物 organism	Thermoplasma acidophilum
NCBI 分类编号 ncbi_taxonomy_id	2303
宿主生物 host_organism	Escherichia coli

Entity 2 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	1

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	1

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	353

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1z1wa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.98 — Zn aminopeptidase N-terminal domain
超家族 Superfamily superfamily	b.98.1 — Zn aminopeptidase N-terminal domain
家族 Family family	b.98.1.1 — Zn aminopeptidase N-terminal domain

结构域编号 domain_id	d1z1wa2
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.92.1.13 — Zn aminopeptidase catalytic domain

结构域编号 domain_id	d1z1wa3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.30 — Zn aminopeptidase insert domain
家族 Family family	b.1.30.1 — Zn aminopeptidase insert domain

结构域编号 domain_id	d1z1wa4
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.118 — alpha-alpha superhelix
超家族 Superfamily superfamily	a.118.1 — ARM repeat
家族 Family family	a.118.1.26 — ERAP1 C-terminal-like

CATH v4.4 (3 domains)

结构域编号 domain_id	1z1wA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1730 — tricorn interacting facor f3 domain

结构域编号 domain_id	1z1wA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	390 — Neutral Protease; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Neutral Protease Domain 2

结构域编号 domain_id	1z1wA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1910 —

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7. 引用文献 (1)

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晶胞边长 a length_a	104.786 Å
晶胞边长 b length_b	104.786 Å
晶胞边长 c length_c	137.348 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	2.700 Å
最低分辨率 resolution_low	19.920 Å
R 因子 r_factor	0.2230
R_work r_work	0.2230
R_free r_free	0.2950

fit	/app/data/saxs_computation/z1/1z1w/1z1w.fit
pddf	/app/data/pr_computation/z1/1z1w/1z1w.pr.out
profile	/app/data/saxs_computation/z1/1z1w/1z1w.dat