SAXSdb — 1o2d

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1o2d
沉积日期 deposition_date	2003-02-27
结构标题 title	Crystal structure of Alcohol dehydrogenase, iron-containing (TM0920) from Thermotoga maritima at 1.30 A resolution
关键词 keywords	;TM0920, ALCOHOL DEHYDROGENASE, IRON-CONTAINING, STRUCTURAL GENOMICS, JCSG, PSI, PROTEIN STRUCTURE INITIATIVE, JOINT CENTER FOR STRUCTURAL GENOMICS, 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	33.02 Å
回转半径 Rg (电子) rg_electron	32.64 Å
零角强度 I(0) i0	104288000.00
分子量 molecular_weight	81402.0 kDa
排除体积 excluded_volume	101370 Å³
包络体积 envelope_volume	126290 Å³
水化壳体积 shell_volume	32268 Å³
包络直径 envelope_diameter	104.3 Å
壳层 Rg shell_rg	39.67 Å
包络 Rg envelope_rg	31.84 Å
形状 Rg shape_rg	32.65 Å
总 Rg total_rg	33.16 Å
总原子数 total_atoms	5641
残基数 n_residues	697
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	104.0 Å
Rg (实空间) rg_real	33.13 Å
Rg 误差 (实空间) rg_real_error	1.03 Å
I(0) (实空间) i0_real	1.0430e+08
I(0) 误差 (实空间) i0_real_error	1.7410e+06
Rg (倒空间) rg_reciprocal	33.09 Å
I(0) (倒空间) i0_reciprocal	104300000.0000
解质量估计 total_estimate	0.8573
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	26.0 Å
偏度 Skewness skewness	0.240
峰度 Kurtosis kurtosis	-0.874
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35890000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.829; Smooth: 0.856

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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 (5)

Entity 1 polymer

描述 description	Alcohol dehydrogenase, iron-containing
分子量 formula_weight	41942.3 kDa
EC 编号 ec_number	1.1.1.1
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	6604

MGSDKIHHHHHHVWEFYMPTDVFFGEKILEKRGNIIDLLGKRALVVTGKSSSKKNGSLDDLKKLLDETEISYEIFDEVEENPSFDNVMKAVERYRNDSFDFVVGLGGGSPMDFAKAVAVLLKEKDLSVEDLYDREKVKHWLPVVEIPTTAGTGSEVTPYSILTDPEGNKRGCTLMFPVYAFLDPRYTYSMSDELTLSTGVDALSHAVEGYLSRKSTPPSDALAIEAMKIIHRNLPKAIEGNREARKKMFVASCLAGMVIAQTGTTLAHALGYPLTTEKGIKHGKATGMVLPFVMEVMKEEIPEKVDTVNHIFGGSLLKFLKELGLYEKVAVSSEELEKWVEKGSRAKHLKNTPGTFTPEKIRNIYREALGV

来源 Source

来源生物 organism	Thermotoga maritima
NCBI 分类编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
分子量 formula_weight	743.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
分子量 formula_weight	122.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	892

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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	d1o2da1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.22 — Dehydroquinate synthase-like
超家族 Superfamily superfamily	e.22.1 — Dehydroquinate synthase-like
家族 Family family	e.22.1.2 — Iron-containing alcohol dehydrogenase

结构域编号 domain_id	d1o2da2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1o2db1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.22 — Dehydroquinate synthase-like
超家族 Superfamily superfamily	e.22.1 — Dehydroquinate synthase-like
家族 Family family	e.22.1.2 — Iron-containing alcohol dehydrogenase

结构域编号 domain_id	d1o2db2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

结构域编号 domain_id	1o2dA01
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	1970 —

结构域编号 domain_id	1o2dA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1090 — Dehydroquinate synthase-like, alpha domain
同源超家族 H-superfamily homologous superfamily	10 — Dehydroquinate synthase-like - alpha domain

结构域编号 domain_id	1o2dB01
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	1970 —

结构域编号 domain_id	1o2dB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1090 — Dehydroquinate synthase-like, alpha domain
同源超家族 H-superfamily homologous superfamily	10 — Dehydroquinate synthase-like - alpha domain

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7. 引用文献 (1)

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晶胞边长 a length_a	58.047 Å
晶胞边长 b length_b	85.283 Å
晶胞边长 c length_c	72.080 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.29 °
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	1.300 Å
最低分辨率 resolution_low	38.190 Å
R 因子 r_factor	0.1390
R_work r_work	0.1370
R_free r_free	0.1700

fit	/app/data/saxs_computation/o2/1o2d/1o2d.fit
pddf	/app/data/pr_computation/o2/1o2d/1o2d.pr.out
profile	/app/data/saxs_computation/o2/1o2d/1o2d.dat

Crystal structure of Alcohol dehydrogenase, iron-containing (TM0920) from Thermotoga maritima at 1.30 A 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