SAXSdb — 1xtl

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1xtl
沉积日期 deposition_date	2004-10-22
结构标题 title	Crystal structure of P104H mutant of SOD-like protein from Bacillus subtilis.
关键词 keywords	SOD, Cu-Zn SOD, SOD-like, superoxide dismutase mutants, structural genomics, UNKNOWN FUNCTION; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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	30.08 Å
回转半径 Rg (电子) rg_electron	30.12 Å
零角强度 I(0) i0	78390600.00
分子量 molecular_weight	65363.0 kDa
排除体积 excluded_volume	79694 Å³
包络体积 envelope_volume	102610 Å³
水化壳体积 shell_volume	29985 Å³
包络直径 envelope_diameter	107.7 Å
壳层 Rg shell_rg	35.28 Å
包络 Rg envelope_rg	29.99 Å
形状 Rg shape_rg	30.15 Å
总 Rg total_rg	30.48 Å
总原子数 total_atoms	4558
残基数 n_residues	608
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	103.5 Å
Rg (实空间) rg_real	30.29 Å
Rg 误差 (实空间) rg_real_error	1.08 Å
I(0) (实空间) i0_real	7.8390e+07
I(0) 误差 (实空间) i0_real_error	1.1930e+06
Rg (倒空间) rg_reciprocal	30.20 Å
I(0) (倒空间) i0_reciprocal	78390000.0000
解质量估计 total_estimate	0.8415
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	25.4 Å
偏度 Skewness skewness	0.498
峰度 Kurtosis kurtosis	-0.306
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35230000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.744; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.778; Smooth: 0.937

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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	Hypothetical superoxide dismutase-like protein yojM
分子量 formula_weight	18779.8 kDa
突变 mutation	P83H
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	B,A,C,D
原子数 atom_count	4865

KPPDPPNRVPEKKVVETSAFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGHFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALLGNNEKQ

来源 Source

来源生物 organism	Bacillus subtilis
NCBI 分类编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	COPPER (II) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

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	307

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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	d1xtla_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
家族 Family family	b.1.8.0 — automated matches

结构域编号 domain_id	d1xtlb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
家族 Family family	b.1.8.0 — automated matches

结构域编号 domain_id	d1xtlc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
家族 Family family	b.1.8.0 — automated matches

结构域编号 domain_id	d1xtld_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
家族 Family family	b.1.8.0 — automated matches

CATH v4.4 (4 domains)

结构域编号 domain_id	1xtlA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

结构域编号 domain_id	1xtlB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

结构域编号 domain_id	1xtlC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

结构域编号 domain_id	1xtlD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

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7. 引用文献 (2)

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晶胞边长 a length_a	52.147 Å
晶胞边长 b length_b	56.586 Å
晶胞边长 c length_c	59.118 Å
晶胞夹角 α angle_alpha	78.24 °
晶胞夹角 β angle_beta	89.91 °
晶胞夹角 γ angle_gamma	85.47 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	38.920 Å
R 因子 r_factor	0.2374
R_work r_work	0.2319
R_free r_free	0.2992

fit	/app/data/saxs_computation/xt/1xtl/1xtl.fit
pddf	/app/data/pr_computation/xt/1xtl/1xtl.pr.out
profile	/app/data/saxs_computation/xt/1xtl/1xtl.dat

Crystal structure of P104H mutant of SOD-like protein from Bacillus subtilis.

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 non-polymer

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)