2fok

STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI

Method: X-RAY DIFFRACTION D_max: 109.2 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	2fok
沉积日期 deposition_date	1998-03-30
结构标题 title	STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI
关键词 keywords	;NUCLEIC ACID RECOGNITION, DNA-BINDING PROTEIN, TYPE IIS RESTRICTION ENDONUCLEASE, DEOXYRIBONUCLEASE, DNA HYDROLYSIS, DNA CLEAVAGE, METALLOENZYME, METAL ION CATALYSIS ;; NUCLEIC ACID RECOGNITION
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	35.54 Å
回转半径 Rg (电子) rg_electron	34.95 Å
零角强度 I(0) i0	228849000.00
分子量 molecular_weight	126170.0 kDa
排除体积 excluded_volume	159840 Å³
包络体积 envelope_volume	209530 Å³
水化壳体积 shell_volume	48810 Å³
包络直径 envelope_diameter	114.5 Å
壳层 Rg shell_rg	43.02 Å
包络 Rg envelope_rg	33.71 Å
形状 Rg shape_rg	34.92 Å
总 Rg total_rg	35.62 Å
总原子数 total_atoms	8911
残基数 n_residues	1118
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	109.2 Å
Rg (实空间) rg_real	35.36 Å
Rg 误差 (实空间) rg_real_error	0.70 Å
I(0) (实空间) i0_real	2.2880e+08
I(0) 误差 (实空间) i0_real_error	3.6400e+06
Rg (倒空间) rg_reciprocal	35.48 Å
I(0) (倒空间) i0_reciprocal	228900000.0000
解质量估计 total_estimate	0.9081
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	48.5 Å
偏度 Skewness skewness	0.058
峰度 Kurtosis kurtosis	-0.658
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	41240000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.938

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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 (2)

Entity 1 polymer

描述 description	FOKI RESTRICTION ENDONUCLEASE
分子量 formula_weight	65833.6 kDa
EC 编号 ec_number	3.1.21.4
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	9427

MVSKIRTFGWVQNPGKFENLKRVVQVFDRNSKVHNEVKNIKIPTLVKESKIQKELVAIMNQHDLIYTYKELVGTGTSIRSEAPCDAIIQATIADQGNKKGYIDNWSSDGFLRWAHALGFIEYINKSDSFVITDVGLAYSKSADGSAIEKEILIEAISSYPPAIRILTLLEDGQHLTKFDLGKNLGFSGESGFTSLPEGILLDTLANAMPKDKGEIRNNWEGSSDKYARMIGGWLDKLGLVKQGKKEFIIPTLGKPDNKEFISHAFKITGEGLKVLRRAKGSTKFTRVPKRVYWEMLATNLTDKEYVRTRRALILEILIKAGSLKIEQIQDNLKKLGFDEVIETIENDIKGLINTGIFIEIKGRFYQLKDHILQFVIPNRLGKPDLVKSELEEKKSELRHKLKYVPHEYIELIEIARNSTQDRILEMKVMEFFMKVYGYRGKHLGGSRKPDGAIYTVGSPIDYGVIVDTKAYSGGYNLPIGQADEMQRYVEENQTRNKHINPNEWWKVYPSSVTEFKFLFVSGHFKGNYKAQLTRLNHITNCNGAVLSVEELLIGGEMIKAGTLTLEEVRRKFNNGEINF

来源 Source

来源生物 organism	Planomicrobium okeanokoites
NCBI 分类编号 ncbi_taxonomy_id	244
宿主生物 host_organism	Escherichia coli

Entity 2 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	516

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2foka1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.12 — Restriction endonuclease FokI, N-terminal (recognition) domain

结构域编号 domain_id	d2foka2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.12 — Restriction endonuclease FokI, N-terminal (recognition) domain

结构域编号 domain_id	d2foka3
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.12 — Restriction endonuclease FokI, N-terminal (recognition) domain

结构域编号 domain_id	d2foka4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.52 — Restriction endonuclease-like
超家族 Superfamily superfamily	c.52.1 — Restriction endonuclease-like
家族 Family family	c.52.1.12 — Restriction endonuclease FokI, C-terminal (catalytic) domain

结构域编号 domain_id	d2fokb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.12 — Restriction endonuclease FokI, N-terminal (recognition) domain

结构域编号 domain_id	d2fokb2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.12 — Restriction endonuclease FokI, N-terminal (recognition) domain

结构域编号 domain_id	d2fokb3
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.12 — Restriction endonuclease FokI, N-terminal (recognition) domain

结构域编号 domain_id	d2fokb4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.52 — Restriction endonuclease-like
超家族 Superfamily superfamily	c.52.1 — Restriction endonuclease-like
家族 Family family	c.52.1.12 — Restriction endonuclease FokI, C-terminal (catalytic) domain

CATH v4.4 (6 domains)

结构域编号 domain_id	2fokA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	241 — FokI Restriction Endonuclease; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Foki Restriction Endonuclease, Chain A, domain 1

结构域编号 domain_id	2fokA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	2fokA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	91 — Restriction Endonuclease
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	2fokB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	241 — FokI Restriction Endonuclease; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Foki Restriction Endonuclease, Chain A, domain 1

结构域编号 domain_id	2fokB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	2fokB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	91 — Restriction Endonuclease
同源超家族 H-superfamily homologous superfamily	30 —

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7. 引用文献 (2)

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晶胞边长 a length_a	54.010 Å
晶胞边长 b length_b	137.170 Å
晶胞边长 c length_c	188.870 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	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	6.000 Å
R 因子 r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.3060

fit	/app/data/saxs_computation/fo/2fok/2fok.fit
pddf	/app/data/pr_computation/fo/2fok/2fok.pr.out
profile	/app/data/saxs_computation/fo/2fok/2fok.dat

STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI

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