SAXSdb — 1fdo

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fdo
沉积日期 deposition_date	1997-01-27
结构标题 title	OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI
关键词 keywords	;OXIDOREDUCTASE, SELENIUM, SELENOCYSTEINE, SECYS, MOLYBDENUM, MOLYBDOPTERIN, MPT, MOLYBDOPTERIN GUANINE DINUCLEOTIDE, MGD, IRON SULFUR CLUSTER, FE4S4, FORMATE, DEHYDROGENASE, ANAEROBIC ;; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	25.35 Å
回转半径 Rg (电子) rg_electron	24.56 Å
零角强度 I(0) i0	114902000.00
分子量 molecular_weight	81292.0 kDa
排除体积 excluded_volume	100230 Å³
包络体积 envelope_volume	111630 Å³
水化壳体积 shell_volume	35823 Å³
包络直径 envelope_diameter	79.7 Å
壳层 Rg shell_rg	33.61 Å
包络 Rg envelope_rg	24.98 Å
形状 Rg shape_rg	24.61 Å
总 Rg total_rg	25.26 Å
总原子数 total_atoms	5678
残基数 n_residues	715
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	77.4 Å
Rg (实空间) rg_real	25.22 Å
Rg 误差 (实空间) rg_real_error	0.32 Å
I(0) (实空间) i0_real	1.1490e+08
I(0) 误差 (实空间) i0_real_error	1.4290e+06
Rg (倒空间) rg_reciprocal	25.26 Å
I(0) (倒空间) i0_reciprocal	114900000.0000
解质量估计 total_estimate	0.9049
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	30.7 Å
偏度 Skewness skewness	0.200
峰度 Kurtosis kurtosis	-0.444
角度范围 angular_range	— – 0.3150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	30280000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.987

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	FORMATE DEHYDROGENASE H
分子量 formula_weight	79465.7 kDa
EC 编号 ec_number	1.2.1.2
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	5742

MKKVVTVCPYCASGCKINLVVDNGKIVRAEAAQGKTNQGTLCLKGYYGWDFINDTQILTPRLKTPMIRRQRGGKLEPVSWDEALNYVAERLSAIKEKYGPDAIQTTGSSRGTGNETNYVMQKFARAVIGTNNVDCCARVUHGPSVAGLHQSVGNGAMSNAINEIDNTDLVFVFGYNPADSHPIVANHVINAKRNGAKIIVCDPRKIETARIADMHIALKNGSNIALLNAMGHVIIEENLYDKAFVASRTEGFEEYRKIVEGYTPESVEDITGVSASEIRQAARMYAQAKSAAILWGMGVTQFYQGVETVRSLTSLAMLTGNLGKPHAGVNPVRGQNNVQGACDMGALPDTYPGYQYVKDPANREKFAKAWGVESLPAHTGYRISELPHRAAHGEVRAAYIMGEDPLQTDAELSAVRKAFEDLELVIVQDIFMTKTASAADVILPSTSWGEHEGVFTAADRGFQRFFKAVEPKWDLKTDWQIISEIATRMGYPMHYNNTQEIWDELRHLCPDFYGATYEKMGELGFIQWPCRDTSDADQGTSYLFKEKFDTPNGLAQFFTCDWVAPIDKLTDEYPMVLSTVREVGHYSCRSMTGNCAALAALADEPGYAQINTEDAKRLGIEDEALVWVHSRKGKIITRAQVSDRPNKGAIYMTYQWWIGACNELVTENLSPITKTPEYKYCAVRVEPIADQRAAEQYVIDEYNKLKTRLREAALA

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	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
分子量 formula_weight	740.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	MOLYBDENUM(VI) ION
分子量 formula_weight	95.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	64

▼

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1fdoa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain

结构域编号 domain_id	d1fdoa2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
超家族 Superfamily superfamily	c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
家族 Family family	c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3

CATH v4.4 (5 domains)

结构域编号 domain_id	1fdoA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily	90 — ADC-like domains

结构域编号 domain_id	1fdoA02
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	740 —

结构域编号 domain_id	1fdoA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	228 — Dimethylsulfoxide Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dimethylsulfoxide Reductase, domain 2

结构域编号 domain_id	1fdoA04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1fdoA05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	460 — Single helix bin

▶

7. 引用文献 (2)

▶

晶胞边长 a length_a	146.600 Å
晶胞边长 b length_b	146.600 Å
晶胞边长 c length_c	81.100 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	8

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	6.000 Å
R 因子 r_factor	0.1920
R_work r_work	0.1920
R_free r_free	0.2810

fit	/app/data/saxs_computation/fd/1fdo/1fdo.fit
pddf	/app/data/pr_computation/fd/1fdo/1fdo.pr.out
profile	/app/data/saxs_computation/fd/1fdo/1fdo.dat

OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI

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