SAXSdb — 1ixb

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ixb
沉积日期 deposition_date	2002-06-18
结构标题 title	CRYSTAL STRUCTURE OF THE E. COLI MANGANESE(II) SUPEROXIDE DISMUTASE MUTANT Y174F AT 0.90 ANGSTROMS RESOLUTION.
关键词 keywords	MANGANESE(II) SUPEROXIDE DISMUTASE, Y174F MUTANT, HYDROGEN BOND REACTIVITY, ULTRAHIGH RESOLUTION, 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	22.95 Å
回转半径 Rg (电子) rg_electron	22.24 Å
零角强度 I(0) i0	34853100.00
分子量 molecular_weight	46040.0 kDa
排除体积 excluded_volume	57721 Å³
包络体积 envelope_volume	66352 Å³
水化壳体积 shell_volume	24719 Å³
包络直径 envelope_diameter	76.7 Å
壳层 Rg shell_rg	29.20 Å
包络 Rg envelope_rg	22.45 Å
形状 Rg shape_rg	22.20 Å
总 Rg total_rg	23.19 Å
总原子数 total_atoms	3258
残基数 n_residues	410
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	77.8 Å
Rg (实空间) rg_real	22.90 Å
Rg 误差 (实空间) rg_real_error	0.50 Å
I(0) (实空间) i0_real	3.4850e+07
I(0) 误差 (实空间) i0_real_error	5.1060e+05
Rg (倒空间) rg_reciprocal	22.91 Å
I(0) (倒空间) i0_reciprocal	34850000.0000
解质量估计 total_estimate	0.8787
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	26.3 Å
偏度 Skewness skewness	0.308
峰度 Kurtosis kurtosis	-0.292
角度范围 angular_range	— – 0.3450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11710000.0000
实空间数据点数 n_real_points	66
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.993

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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	SUPEROXIDE DISMUTASE
分子量 formula_weight	22980.9 kDa
EC 编号 ec_number	1.15.1.1
突变 mutation	Y174F
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	4344

SYTLPSLPYAYDALEPHFDKQTMEIHHTKHHQTYVNNANAALESLPEFANLPVEELITKLDQLPADKKTVLRNNAGGHANHSLFWKGLKKGTTLQGDLKAAIERDFGSVDNFKAEFEKAAASRFGSGWAWLVLKGDKLAVVSTANQDSPLMGEAISGASGFPIMGLDVWEHAYFLKFQNRRPDYIKEFWNVVNWDEAAARFAAKK

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	MANGANESE ION, 1 HYDROXYL COORDINATED
分子量 formula_weight	71.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	925

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1ixba1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.2 — Long alpha-hairpin
超家族 Superfamily superfamily	a.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
家族 Family family	a.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain

结构域编号 domain_id	d1ixba2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
超家族 Superfamily superfamily	d.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
家族 Family family	d.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain

结构域编号 domain_id	d1ixbb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.2 — Long alpha-hairpin
超家族 Superfamily superfamily	a.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
家族 Family family	a.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain

结构域编号 domain_id	d1ixbb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
超家族 Superfamily superfamily	d.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
家族 Family family	d.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1ixbA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	990 — Fe,Mn superoxide dismutase (SOD) domain

结构域编号 domain_id	1ixbA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	55 — 3-Layer(bab) Sandwich
拓扑 Topology topology	40 — minor pseudopilin epsh fold
同源超家族 H-superfamily homologous superfamily	20 — Iron/manganese superoxide dismutase, C-terminal domain

结构域编号 domain_id	1ixbB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	990 — Fe,Mn superoxide dismutase (SOD) domain

结构域编号 domain_id	1ixbB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	55 — 3-Layer(bab) Sandwich
拓扑 Topology topology	40 — minor pseudopilin epsh fold
同源超家族 H-superfamily homologous superfamily	20 — Iron/manganese superoxide dismutase, C-terminal domain

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7. 引用文献 (3)

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晶胞边长 a length_a	46.815 Å
晶胞边长 b length_b	45.832 Å
晶胞边长 c length_c	96.187 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.20 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	0.900 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1109
R_work r_work	0.1107
R_free r_free	0.1264

fit	/app/data/saxs_computation/ix/1ixb/1ixb.fit
pddf	/app/data/pr_computation/ix/1ixb/1ixb.pr.out
profile	/app/data/saxs_computation/ix/1ixb/1ixb.dat

CRYSTAL STRUCTURE OF THE E. COLI MANGANESE(II) SUPEROXIDE DISMUTASE MUTANT Y174F AT 0.90 ANGSTROMS RESOLUTION.

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