2ffl

Crystal Structure of Dicer from Giardia intestinalis

Method: X-RAY DIFFRACTION D_max: 186.6 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2ffl
沉积日期 deposition_date	2005-12-19
结构标题 title	Crystal Structure of Dicer from Giardia intestinalis
关键词 keywords	RNA interference; RNAi; PAZ domain, TRANSLATION, HYDROLASE; TRANSLATION,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	55.13 Å
回转半径 Rg (电子) rg_electron	55.24 Å
零角强度 I(0) i0	1386310000.00
分子量 molecular_weight	319330.0 kDa
排除体积 excluded_volume	402800 Å³
包络体积 envelope_volume	596490 Å³
水化壳体积 shell_volume	92063 Å³
包络直径 envelope_diameter	198.0 Å
壳层 Rg shell_rg	55.62 Å
包络 Rg envelope_rg	54.99 Å
形状 Rg shape_rg	55.26 Å
总 Rg total_rg	55.17 Å
总原子数 total_atoms	22372
残基数 n_residues	2895
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	186.6 Å
Rg (实空间) rg_real	55.21 Å
Rg 误差 (实空间) rg_real_error	1.90 Å
I(0) (实空间) i0_real	1.3860e+09
I(0) 误差 (实空间) i0_real_error	2.8520e+07
Rg (倒空间) rg_reciprocal	55.05 Å
I(0) (倒空间) i0_reciprocal	1386000000.0000
解质量估计 total_estimate	0.8497
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	70.8 Å
偏度 Skewness skewness	0.391
峰度 Kurtosis kurtosis	-0.114
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	104400000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.550

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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	Dicer
分子量 formula_weight	82690.1 kDa
EC 编号 ec_number	3.1.26.3
突变 mutation	N-terminal GA residues
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	22426

GAMHALGHCCTVVTTRGPSHWLLLLDTHLGTLPGFKVSAGRGLPAAEVYFEAGPRVSLSRTDATIVAVYQSILFQLLGPTFPASWTEIGATMPHNEYTFPRFISNPPQFATLAFLPLLSPTSPLDLRALMVTAQLMCDAKRLSDEYTDYSTLSASLHGRMVATPEISWSLYVVLGIDSTQTSLSYFTRANESITYMRYYATAHNIHLRAADLPLVAAVRLDDLKDHQIPAPGSWDDLAPKLRFLPPELCLLLPDEFDLIRVQALQFLPEIAKHICDIQNTICALDKSFPDCGRIGGERYFAITAGLRLDQGRGRGLAGWRTPFGPFGVSHTDVFQRLELLGDAVLGFIVTARLLCLFPDASVGTLVELKMELVRNEALNYLVQTLGLPQLAEFSNNLVAKSKTWADMYEEIVGSIFTGPNGIYGCEEFLAKTLMSPEHSKTVGSACPDAVTKASKRVCMGEAGAHEFRSLVDYACEQGISVFCSSRVSTMFLERLRDIPAEDMLDWYRLGIQFSHRSGLSGPGGVVSVIDIMTHLARGLWLGSPGFYVEQQTDKNESACPPTIPVLYIYHRSVQCPVLYGSLTETPTGPVASKVLALYEKILAYESSGGSKHIAAQTVSRSLAVPIPSGTIPFLIRLLQIALTPHVYQKLELLGDAFLKCSLALHLHALHPTLTEGALTRMRQSAETNSVLGRLTKRFPSVVSEVIIESHPKIQPDSKVYGDTFEAILAAILLACGEEAAGAFVREHVLPQVVADA

来源 Source

来源生物 organism	Giardia intestinalis
NCBI 分类编号 ncbi_taxonomy_id	5741
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	39

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	54

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6. 折叠分类 (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

结构域编号 domain_id	2fflA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	260 — paz domain
同源超家族 H-superfamily homologous superfamily	10 — paz domain

结构域编号 domain_id	2fflA03
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	1440 —

结构域编号 domain_id	2fflA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1520 — Ribonuclease iii, N-terminal Endonuclease Domain; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease III domain

结构域编号 domain_id	2fflA05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
同源超家族 H-superfamily homologous superfamily	150 —

结构域编号 domain_id	2fflA06
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1520 — Ribonuclease iii, N-terminal Endonuclease Domain; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease III domain

结构域编号 domain_id	2fflB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	260 — paz domain
同源超家族 H-superfamily homologous superfamily	10 — paz domain

结构域编号 domain_id	2fflB03
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	1440 —

结构域编号 domain_id	2fflB04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1520 — Ribonuclease iii, N-terminal Endonuclease Domain; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease III domain

结构域编号 domain_id	2fflB05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
同源超家族 H-superfamily homologous superfamily	150 —

结构域编号 domain_id	2fflB06
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1520 — Ribonuclease iii, N-terminal Endonuclease Domain; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease III domain

结构域编号 domain_id	2fflC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	260 — paz domain
同源超家族 H-superfamily homologous superfamily	10 — paz domain

结构域编号 domain_id	2fflC03
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	1440 —

结构域编号 domain_id	2fflC04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1520 — Ribonuclease iii, N-terminal Endonuclease Domain; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease III domain

结构域编号 domain_id	2fflC05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
同源超家族 H-superfamily homologous superfamily	150 —

结构域编号 domain_id	2fflC06
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1520 — Ribonuclease iii, N-terminal Endonuclease Domain; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease III domain

结构域编号 domain_id	2fflD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	260 — paz domain
同源超家族 H-superfamily homologous superfamily	10 — paz domain

结构域编号 domain_id	2fflD03
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	1440 —

结构域编号 domain_id	2fflD04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1520 — Ribonuclease iii, N-terminal Endonuclease Domain; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease III domain

结构域编号 domain_id	2fflD05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
同源超家族 H-superfamily homologous superfamily	150 —

结构域编号 domain_id	2fflD06
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1520 — Ribonuclease iii, N-terminal Endonuclease Domain; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease III domain

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7. 引用文献 (1)

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晶胞边长 a length_a	155.515 Å
晶胞边长 b length_b	174.101 Å
晶胞边长 c length_c	152.910 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	16

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	3.330 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2445
R_work r_work	0.2429
R_free r_free	0.2745

fit	/app/data/saxs_computation/ff/2ffl/2ffl.fit
pddf	/app/data/pr_computation/ff/2ffl/2ffl.pr.out
profile	/app/data/saxs_computation/ff/2ffl/2ffl.dat