1qqw

CRYSTAL STRUCTURE OF HUMAN ERYTHROCYTE CATALASE

Method: X-RAY DIFFRACTION D_max: 111.8 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	1qqw
沉积日期 deposition_date	1999-06-09
结构标题 title	CRYSTAL STRUCTURE OF HUMAN ERYTHROCYTE CATALASE
关键词 keywords	HEME PROTEIN, LATTICE CONTACT, WATER, NO NADP, 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	36.63 Å
回转半径 Rg (电子) rg_electron	35.96 Å
零角强度 I(0) i0	798723000.00
分子量 molecular_weight	229300.0 kDa
排除体积 excluded_volume	285440 Å³
包络体积 envelope_volume	337320 Å³
水化壳体积 shell_volume	72621 Å³
包络直径 envelope_diameter	116.0 Å
壳层 Rg shell_rg	46.07 Å
包络 Rg envelope_rg	35.94 Å
形状 Rg shape_rg	35.95 Å
总 Rg total_rg	36.52 Å
总原子数 total_atoms	16225
残基数 n_residues	1997
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	111.8 Å
Rg (实空间) rg_real	36.38 Å
Rg 误差 (实空间) rg_real_error	0.61 Å
I(0) (实空间) i0_real	7.9870e+08
I(0) 误差 (实空间) i0_real_error	1.1480e+07
Rg (倒空间) rg_reciprocal	36.54 Å
I(0) (倒空间) i0_reciprocal	798800000.0000
解质量估计 total_estimate	0.8969
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	46.8 Å
偏度 Skewness skewness	0.137
峰度 Kurtosis kurtosis	-0.504
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	299500000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.904

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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	CATALASE
分子量 formula_weight	59837.0 kDa
EC 编号 ec_number	1.11.1.6
来源方法 src_method	nat
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	16618

MADSRDPASDQMQHWKEQRAAQKADVLTTGAGNPVGDKLNVITVGPRGPLLVQDVVFTDEMAHFDRERIPERVVHAKGAGAFGYFEVTHDITKYSKAKVFEHIGKKTPIAVRFSTVAGESGSADTVRDPRGFAVKFYTEDGNWDLVGNNTPIFFIRDPILFPSFIHSQKRNPQTHLKDPDMVWDFWSLRPESLHQVSFLFSDRGIPDGHRHMNGYGSHTFKLVNANGEAVYCKFHYKTDQGIKNLSVEDAARLSQEDPDYGIRDLFNAIATGKYPSWTFYIQVMTFNQAETFPFNPFDLTKVWPHKDYPLIPVGKLVLNRNPVNYFAEVEQIAFDPSNMPPGIEASPDKMLQGRLFAYPDTHRHRLGPNYLHIPVNCPYRARVANYQRDGPMCMQDNQGGAPNYYPNSFGAPEQQPSALEHSIQYSGEVRRFNTANDDNVTQVRAFYVNVLNEEQRKRLCENIAGHLKDAQIFIQKKAVKNFTEVHPDYGSHIQALLDKYNAEKPKNAIHTFVQSGSHLAAREKANL

Entity 2 non-polymer

描述 description	PROTOPORPHYRIN IX CONTAINING FE
分子量 formula_weight	616.5 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	393

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1qqwa_
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	d1qqwb_
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	d1qqwc_
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	d1qqwd_
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	1qqwA01
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	91 — Cytochrome C Oxidase; Chain J
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1qqwA02
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	1qqwA03
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	60 —

结构域编号 domain_id	1qqwB01
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	91 — Cytochrome C Oxidase; Chain J
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1qqwB02
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	1qqwB03
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	60 —

结构域编号 domain_id	1qqwC01
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	91 — Cytochrome C Oxidase; Chain J
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1qqwC02
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	1qqwC03
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	60 —

结构域编号 domain_id	1qqwD01
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	91 — Cytochrome C Oxidase; Chain J
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1qqwD02
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	1qqwD03
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	60 —

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7. 引用文献 (1)

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晶胞边长 a length_a	84.904 Å
晶胞边长 b length_b	141.674 Å
晶胞边长 c length_c	232.460 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 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.750 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.2110
R_work r_work	0.2060
R_free r_free	0.2720

fit	/app/data/saxs_computation/qq/1qqw/1qqw.fit
pddf	/app/data/pr_computation/qq/1qqw/1qqw.pr.out
profile	/app/data/saxs_computation/qq/1qqw/1qqw.dat

CRYSTAL STRUCTURE OF HUMAN ERYTHROCYTE CATALASE

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