SAXSdb — 2fsv

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2fsv
沉积日期 deposition_date	2006-01-23
结构标题 title	Structure of transhydrogenase (dI.D135N.NAD+)2(dIII.E155W.NADP+)1 asymmetric complex
关键词 keywords	NAD(P) TRANSHYDROGENASE SUBUNITS, NAD+, NADP+, OXIDOREDUCTASE; 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	31.42 Å
回转半径 Rg (电子) rg_electron	30.74 Å
零角强度 I(0) i0	145198000.00
分子量 molecular_weight	96958.0 kDa
排除体积 excluded_volume	122140 Å³
包络体积 envelope_volume	150500 Å³
水化壳体积 shell_volume	40707 Å³
包络直径 envelope_diameter	104.1 Å
壳层 Rg shell_rg	37.90 Å
包络 Rg envelope_rg	30.89 Å
形状 Rg shape_rg	30.73 Å
总 Rg total_rg	31.39 Å
总原子数 total_atoms	6779
残基数 n_residues	901
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	101.4 Å
Rg (实空间) rg_real	31.38 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	1.4520e+08
I(0) 误差 (实空间) i0_real_error	2.4490e+06
Rg (倒空间) rg_reciprocal	31.40 Å
I(0) (倒空间) i0_reciprocal	145200000.0000
解质量估计 total_estimate	0.8946
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	38.5 Å
偏度 Skewness skewness	0.304
峰度 Kurtosis kurtosis	-0.402
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	124000000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.905

▶

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

▶

5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	NAD(P) transhydrogenase subunit alpha part 1
分子量 formula_weight	40323.8 kDa
EC 编号 ec_number	1.6.1.2
突变 mutation	D135N
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	7169

MKIAIPKERRPGEDRVAISPEVVKKLVGLGFEVIVEQGAGVGASITDDALTAAGATIASTAAQALSQADVVWKVQRPMTAEEGTDEVALIKEGAVLMCHLGALTNRPVVEALTKRKITAYAMELMPRISRAQSMNILSSQSNLAGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGAVVMATDVRAATKEQVESLGGKFITVDDEAMKTAETAGGYAKEMGEEFRKKQAEAVLKELVKTDIAITTALIPGKPAPVLITEEMVTKMKPGSVIIDLAVEAGGNCPLSEPGKIVVKHGVKIVGHTNVPSRVAADASPLFAKNLLNFLTPHVDKDTKTLVMKLEDETVSGTCVTRDGAIVHPALTGQGA

来源 Source

来源生物 organism	Rhodospirillum rubrum
NCBI 分类编号 ncbi_taxonomy_id	1085
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	NAD(P) transhydrogenase subunit beta
分子量 formula_weight	21542.6 kDa
EC 编号 ec_number	1.6.1.2
突变 mutation	E155W
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	C

MNRSIFNVILGGFGSEGGVAAAGGAAGDRSVKAGSAEDAAFIMKNASKVIIVPGYGMAVAQAQHALREMADVLKKEGVEVSYAIHPVAGRMPGHMNVLLAEANVPYDEVFELEEINSSFQTADVAFVIGANDVTNPAAKTDPSSPIYGMPILDVWKAGTVLFIKRSMASGYAGVENELFFRNNTMMLFGDAKKMTEQIVQAMN

来源 Source

来源生物 organism	Rhodospirillum rubrum
NCBI 分类编号 ncbi_taxonomy_id	1085
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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	3

Entity 5 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	1

Entity 6 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	382

▼

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d2fsva1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.4 — Formate/glycerate dehydrogenases, NAD-domain

结构域编号 domain_id	d2fsva2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.12 — Formate/glycerate dehydrogenase catalytic domain-like
家族 Family family	c.23.12.2 — L-alanine dehydrogenase-like

结构域编号 domain_id	d2fsvb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.4 — Formate/glycerate dehydrogenases, NAD-domain

结构域编号 domain_id	d2fsvb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.12 — Formate/glycerate dehydrogenase catalytic domain-like
家族 Family family	c.23.12.2 — L-alanine dehydrogenase-like

结构域编号 domain_id	d2fsvc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.31 — DHS-like NAD/FAD-binding domain
超家族 Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
家族 Family family	c.31.1.4 — Transhydrogenase domain III (dIII)

CATH v4.4 (5 domains)

结构域编号 domain_id	2fsvA01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2fsvA02
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2fsvB01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2fsvB02
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2fsvC00
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	1220 — TPP-binding domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	72.912 Å
晶胞边长 b length_b	73.871 Å
晶胞边长 c length_c	205.172 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 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	31.370 Å
R 因子 r_factor	0.2039
R_work r_work	0.2016
R_free r_free	0.2481

fit	/app/data/saxs_computation/fs/2fsv/2fsv.fit
pddf	/app/data/pr_computation/fs/2fsv/2fsv.pr.out
profile	/app/data/saxs_computation/fs/2fsv/2fsv.dat

Structure of transhydrogenase (dI.D135N.NAD+)2(dIII.E155W.NADP+)1 asymmetric complex

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 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)