1ye9

Crystal structure of proteolytically truncated catalase HPII from E. coli

Method: X-RAY DIFFRACTION D_max: 187.8 Å Quality: REASONABLE

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	1ye9
沉积日期 deposition_date	2004-12-28
结构标题 title	Crystal structure of proteolytically truncated catalase HPII from E. coli
关键词 keywords	catalase HPII, proteolytic truncation, beta barrel core, Oxidoreductase; OXIDOREDUCTASE
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	63.72 Å
回转半径 Rg (电子) rg_electron	64.36 Å
零角强度 I(0) i0	2757220000.00
分子量 molecular_weight	443630.0 kDa
排除体积 excluded_volume	552920 Å³
包络体积 envelope_volume	716550 Å³
水化壳体积 shell_volume	89422 Å³
包络直径 envelope_diameter	205.2 Å
壳层 Rg shell_rg	69.47 Å
包络 Rg envelope_rg	62.85 Å
形状 Rg shape_rg	64.35 Å
总 Rg total_rg	64.48 Å
总原子数 total_atoms	31472
残基数 n_residues	3832
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	187.8 Å
Rg (实空间) rg_real	64.25 Å
Rg 误差 (实空间) rg_real_error	1.52 Å
I(0) (实空间) i0_real	2.7570e+09
I(0) 误差 (实空间) i0_real_error	5.8820e+07
Rg (倒空间) rg_reciprocal	63.14 Å
I(0) (倒空间) i0_reciprocal	2752000000.0000
解质量估计 total_estimate	0.7475
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	45.1 Å
偏度 Skewness skewness	0.309
峰度 Kurtosis kurtosis	-0.975
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	462800000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.628; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.830; Smooth: 0.000

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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	catalase HPII
分子量 formula_weight	25615.7 kDa
EC 编号 ec_number	1.11.1.6
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,I,J,K,L
原子数 atom_count	31715

SENYALTTNQGVRIADDQNSLRAGSRGPTLLEDFILREKITHFDHERIPERIVHARGSAAHGYFQPYKSLSDITKADFLSDPNKITPVFVRFSTVQGGAGSADTVRDIRGFATKFYTEEGIFDLVGNNTPIFFIQDAHKFPDFVHAVKPEPHWAIPQGQSAHDTFWDYVSLQPETLHNVMWAMSDRGIPRSYRTMEGFGIHTFRLINAEGKATFVRFHWKPLAGKA

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	catalase HPII
分子量 formula_weight	30072.5 kDa
EC 编号 ec_number	1.11.1.6
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,F,G,H,M,N,O,P

KLTGRDPDFHRRELWEAIEAGDFPEYELGFQLIPEEDEFKFDFDLLDPTKLIPEELVPVQRVGKMVLNRNPDNFFAENEQAAFHPGHIVPGLDFTNDPLLQGRLFSYTDTQISRLGGPNFHEIPINRPTCPYHNFQRDGMHRMGIDTNPANYEPNSINDNWPRETPPGPKRGGFESYQERVEGNKVRERSPSFGEYYSHPRLFWLSQTPFEQRHIVDGFSFELSKVVRPYIRERVVDQLAHIDLTLAQAVAKNLGIELT

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
分子量 formula_weight	632.5 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	180

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6. 折叠分类 (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

结构域编号 domain_id	1ye9A01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	10 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	30 — Catalase hpii, N-terminal domain-like

结构域编号 domain_id	1ye9A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	470 — catalase hpii fold
同源超家族 H-superfamily homologous superfamily	10 — catalase hpii domain

结构域编号 domain_id	1ye9A03
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	1060 — Catalase HPII, helical domain

结构域编号 domain_id	1ye9B01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	10 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	30 — Catalase hpii, N-terminal domain-like

结构域编号 domain_id	1ye9B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	470 — catalase hpii fold
同源超家族 H-superfamily homologous superfamily	10 — catalase hpii domain

结构域编号 domain_id	1ye9B03
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	1060 — Catalase HPII, helical domain

结构域编号 domain_id	1ye9C01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	10 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	30 — Catalase hpii, N-terminal domain-like

结构域编号 domain_id	1ye9C02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	470 — catalase hpii fold
同源超家族 H-superfamily homologous superfamily	10 — catalase hpii domain

结构域编号 domain_id	1ye9C03
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	1060 — Catalase HPII, helical domain

结构域编号 domain_id	1ye9D01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	10 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	30 — Catalase hpii, N-terminal domain-like

结构域编号 domain_id	1ye9D02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	470 — catalase hpii fold
同源超家族 H-superfamily homologous superfamily	10 — catalase hpii domain

结构域编号 domain_id	1ye9D03
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	1060 — Catalase HPII, helical domain

结构域编号 domain_id	1ye9I01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	10 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	30 — Catalase hpii, N-terminal domain-like

结构域编号 domain_id	1ye9I02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	470 — catalase hpii fold
同源超家族 H-superfamily homologous superfamily	10 — catalase hpii domain

结构域编号 domain_id	1ye9I03
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	1060 — Catalase HPII, helical domain

结构域编号 domain_id	1ye9J01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	10 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	30 — Catalase hpii, N-terminal domain-like

结构域编号 domain_id	1ye9J02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	470 — catalase hpii fold
同源超家族 H-superfamily homologous superfamily	10 — catalase hpii domain

结构域编号 domain_id	1ye9J03
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	1060 — Catalase HPII, helical domain

结构域编号 domain_id	1ye9K01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	10 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	30 — Catalase hpii, N-terminal domain-like

结构域编号 domain_id	1ye9K02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	470 — catalase hpii fold
同源超家族 H-superfamily homologous superfamily	10 — catalase hpii domain

结构域编号 domain_id	1ye9K03
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	1060 — Catalase HPII, helical domain

结构域编号 domain_id	1ye9L01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	10 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	30 — Catalase hpii, N-terminal domain-like

结构域编号 domain_id	1ye9L02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	470 — catalase hpii fold
同源超家族 H-superfamily homologous superfamily	10 — catalase hpii domain

结构域编号 domain_id	1ye9L03
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	1060 — Catalase HPII, helical domain

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7. 引用文献 (1)

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晶胞边长 a length_a	111.011 Å
晶胞边长 b length_b	152.888 Å
晶胞边长 c length_c	135.287 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.54 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	30.000 Å
R 因子 r_factor	0.2198
R_work r_work	0.2171
R_free r_free	0.2690

fit	/app/data/saxs_computation/ye/1ye9/1ye9.fit
pddf	/app/data/pr_computation/ye/1ye9/1ye9.pr.out
profile	/app/data/saxs_computation/ye/1ye9/1ye9.dat

Crystal structure of proteolytically truncated catalase HPII from E. coli

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

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)