1gge

CRYSTAL STRUCTURE OF CATALASE HPII FROM ESCHERICHIA COLI, NATIVE STRUCTURE AT 1.9 A RESOLUTION.

Method: X-RAY DIFFRACTION D_max: 133.8 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	1gge
沉积日期 deposition_date	2000-08-16
结构标题 title	CRYSTAL STRUCTURE OF CATALASE HPII FROM ESCHERICHIA COLI, NATIVE STRUCTURE AT 1.9 A RESOLUTION.
关键词 keywords	BETA BARREL, ALPHA HELICAL DOMAIN, FLAVODOXIN LIKE DOMAIN, 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	41.47 Å
回转半径 Rg (电子) rg_electron	41.19 Å
零角强度 I(0) i0	1561410000.00
分子量 molecular_weight	327340.0 kDa
排除体积 excluded_volume	408850 Å³
包络体积 envelope_volume	475480 Å³
水化壳体积 shell_volume	89703 Å³
包络直径 envelope_diameter	145.7 Å
壳层 Rg shell_rg	50.56 Å
包络 Rg envelope_rg	41.63 Å
形状 Rg shape_rg	41.13 Å
总 Rg total_rg	41.78 Å
总原子数 total_atoms	23160
残基数 n_residues	2908
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	133.8 Å
Rg (实空间) rg_real	41.39 Å
Rg 误差 (实空间) rg_real_error	0.90 Å
I(0) (实空间) i0_real	1.5610e+09
I(0) 误差 (实空间) i0_real_error	2.5290e+07
Rg (倒空间) rg_reciprocal	41.46 Å
I(0) (倒空间) i0_reciprocal	1562000000.0000
解质量估计 total_estimate	0.8009
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	49.3 Å
偏度 Skewness skewness	0.370
峰度 Kurtosis kurtosis	-0.173
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	640000000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 0.991; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; 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 (3)

Entity 1 polymer

描述 description	PROTEIN (CATALASE HPII)
分子量 formula_weight	84271.5 kDa
EC 编号 ec_number	1.11.1.6
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	26368

MSQHNEKNPHQHQSPLHDSSEAKPGMDSLAPEDGSHRPAAEPTPPGAQPTAPGSLKAPDTRNEKLNSLEDVRKGSENYALTTNQGVRIADDQNSLRAGSRGPTLLEDFILREKITHFDHERIPERIVHARGSAAHGYFQPYKSLSDITKADFLSDPNKITPVFVRFSTVQGGAGSADTVRDIRGFATKFYTEEGIFDLVGNNTPIFFIQDAHKFPDFVHAVKPEPHWAIPQGQSAHDTFWDYVSLQPETLHNVMWAMSDRGIPRSYRTMEGFGIHTFRLINAEGKATFVRFHWKPLAGKASLVWDEAQKLTGRDPDFHRRELWEAIEAGDFPEYELGFQLIPEEDEFKFDFDLLDPTKLIPEELVPVQRVGKMVLNRNPDNFFAENEQAAFHPGHIVPGLDFTNDPLLQGRLFSYTDTQISRLGGPNFHEIPINRPTCPYHNFQRDGMHRMGIDTNPANYEPNSINDNWPRETPPGPKRGGFESYQERVEGNKVRERSPSFGEYYSHPRLFWLSQTPFEQRHIVDGFSFELSKVVRPYIRERVVDQLAHIDLTLAQAVAKNLGIELTDDQLNITPPPDVNGLKKDPSLSLYAIPDGDVKGRVVAILLNDEVRSADLLAILKALKAKGVHAKLLYSRMGEVTADDGTVLPIAATFAGAPSLTVDAVIVPCGNIADIADNGDANYYLMEAYKHLKPIALAGDARKFKATIKIADQGEEGIVEADSADGSFMDELLTLMAAHRVWSRIPKIDKIPA

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 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	4

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	3208

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1ggea1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
家族 Family family	c.23.16.3 — Catalase, C-terminal domain

结构域编号 domain_id	d1ggea2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.5 — Heme-dependent catalase-like
超家族 Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
家族 Family family	e.5.1.1 — Heme-dependent catalases

结构域编号 domain_id	d1ggeb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
家族 Family family	c.23.16.3 — Catalase, C-terminal domain

结构域编号 domain_id	d1ggeb2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.5 — Heme-dependent catalase-like
超家族 Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
家族 Family family	e.5.1.1 — Heme-dependent catalases

结构域编号 domain_id	d1ggec1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
家族 Family family	c.23.16.3 — Catalase, C-terminal domain

结构域编号 domain_id	d1ggec2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.5 — Heme-dependent catalase-like
超家族 Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
家族 Family family	e.5.1.1 — Heme-dependent catalases

结构域编号 domain_id	d1gged1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
家族 Family family	c.23.16.3 — Catalase, C-terminal domain

结构域编号 domain_id	d1gged2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.5 — Heme-dependent catalase-like
超家族 Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
家族 Family family	e.5.1.1 — Heme-dependent catalases

CATH v4.4 (12 domains)

结构域编号 domain_id	1ggeA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	180 — Catalase HpII, Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Catalase core domain

结构域编号 domain_id	1ggeA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1370 — Hemocyanin, N-terminal domain
同源超家族 H-superfamily homologous superfamily	20 — Catalase, four-helical domain

结构域编号 domain_id	1ggeA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

结构域编号 domain_id	1ggeB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	180 — Catalase HpII, Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Catalase core domain

结构域编号 domain_id	1ggeB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1370 — Hemocyanin, N-terminal domain
同源超家族 H-superfamily homologous superfamily	20 — Catalase, four-helical domain

结构域编号 domain_id	1ggeB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

结构域编号 domain_id	1ggeC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	180 — Catalase HpII, Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Catalase core domain

结构域编号 domain_id	1ggeC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1370 — Hemocyanin, N-terminal domain
同源超家族 H-superfamily homologous superfamily	20 — Catalase, four-helical domain

结构域编号 domain_id	1ggeC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

结构域编号 domain_id	1ggeD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	180 — Catalase HpII, Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Catalase core domain

结构域编号 domain_id	1ggeD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1370 — Hemocyanin, N-terminal domain
同源超家族 H-superfamily homologous superfamily	20 — Catalase, four-helical domain

结构域编号 domain_id	1ggeD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

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7. 引用文献 (4)

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晶胞边长 a length_a	93.040 Å
晶胞边长 b length_b	132.340 Å
晶胞边长 c length_c	121.200 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	109.63 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	1.890 Å
最低分辨率 resolution_low	87.600 Å
R 因子 r_factor	—
R_work r_work	0.1630
R_free r_free	0.2020

fit	/app/data/saxs_computation/gg/1gge/1gge.fit
pddf	/app/data/pr_computation/gg/1gge/1gge.pr.out
profile	/app/data/saxs_computation/gg/1gge/1gge.dat