SAXSdb — 1of0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1of0
沉积日期 deposition_date	2003-04-03
结构标题 title	CRYSTAL STRUCTURE OF BACILLUS SUBTILIS COTA AFTER 1H SOAKING WITH ABTS
关键词 keywords	OXIDOREDUCTASE, OXIDASE, LACCASE, ENDOSPORE COAT, REACTION CYCLE, SPORULATION, COPPER-DEPENDENT; 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	23.14 Å
回转半径 Rg (电子) rg_electron	22.01 Å
零角强度 I(0) i0	56290900.00
分子量 molecular_weight	58170.0 kDa
排除体积 excluded_volume	72504 Å³
包络体积 envelope_volume	83057 Å³
水化壳体积 shell_volume	29886 Å³
包络直径 envelope_diameter	73.0 Å
壳层 Rg shell_rg	30.26 Å
包络 Rg envelope_rg	22.40 Å
形状 Rg shape_rg	22.02 Å
总 Rg total_rg	22.89 Å
总原子数 total_atoms	4096
残基数 n_residues	503
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	71.8 Å
Rg (实空间) rg_real	22.98 Å
Rg 误差 (实空间) rg_real_error	0.41 Å
I(0) (实空间) i0_real	5.6290e+07
I(0) 误差 (实空间) i0_real_error	7.4510e+05
Rg (倒空间) rg_reciprocal	23.02 Å
I(0) (倒空间) i0_reciprocal	56290000.0000
解质量估计 total_estimate	0.6610
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	29.8 Å
偏度 Skewness skewness	0.127
峰度 Kurtosis kurtosis	-0.471
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	15310000.0000
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: 0.897; Stabil: 0.999; Sysdev: 0.307; Positv: 1.000; Valcen: 0.981; 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 (7)

Entity 1 polymer

描述 description	SPORE COAT PROTEIN A
分子量 formula_weight	58574.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4334

MTLEKFVDALPIPDTLKPVQQSKEKTYYEVTMEECTHQLHRDLPPTRLWGYNGLFPGPTIEVKRNENVYVKWMNNLPSTHFLPIDHTIHHSDSQHEEPEVKTVVHLHGGVTPDDSDGYPEAWFSKDFEQTGPYFKREVYHYPNQQRGAILWYHDHAMALTRLNVYAGLVGAYIIHDPKEKRLKLPSDEYDVPLLITDRTINEDGSLFYPSAPENPSPSLPNPSIVPAFCGETILVNGKVWPYLEVEPRKYRFRVINASNTRTYNLSLDNGGDFIQIGSDGGLLPRSVKLNSFSLAPAERYDIIIDFTAYEGESIILANSAGCGGDVNPETDANIMQFRVTKPLAQKDESRKPKYLASYPSVQHERIQNIRTLKLAGTQDEYGRPVLLLNNKRWHDPVTETPKVGTTEIWSIINPTRGTHPIHLHLVSFRVLDRRPFDIARYQESGELSYTGPAVPPPPSEKGWKDTIQAHAGEVLRIAATFGPYSGRYVWHCHILEHEDYDMMRPMDITDPHK

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 (I) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	CU-O LINKAGE
分子量 formula_weight	79.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	OXYGEN MOLECULE
分子量 formula_weight	32.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	3-ETHYL-2-[(2Z)-2-(3-ETHYL-6-SULFO-1,3-BENZOTHIAZOL-2(3H)-YLIDENE)HYDRAZINO]-6-SULFO-3H-1,3-BENZOTHIAZOL-1-IUM
分子量 formula_weight	514.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 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	238

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1of0a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.3 — Multidomain cupredoxins

结构域编号 domain_id	d1of0a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.3 — Multidomain cupredoxins

结构域编号 domain_id	d1of0a3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.3 — Multidomain cupredoxins

CATH v4.4 (3 domains)

结构域编号 domain_id	1of0A01
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	420 — Cupredoxins - blue copper proteins

结构域编号 domain_id	1of0A02
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	420 — Cupredoxins - blue copper proteins

结构域编号 domain_id	1of0A03
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	420 — Cupredoxins - blue copper proteins

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7. 引用文献 (1)

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晶胞边长 a length_a	102.278 Å
晶胞边长 b length_b	102.278 Å
晶胞边长 c length_c	136.247 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	2.450 Å
最低分辨率 resolution_low	100.000 Å
R 因子 r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2520

fit	/app/data/saxs_computation/of/1of0/1of0.fit
pddf	/app/data/pr_computation/of/1of0/1of0.pr.out
profile	/app/data/saxs_computation/of/1of0/1of0.dat

CRYSTAL STRUCTURE OF BACILLUS SUBTILIS COTA AFTER 1H SOAKING WITH ABTS

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution