1xlt

Crystal structure of Transhydrogenase [(domain I)2:domain III] heterotrimer complex

Method: X-RAY DIFFRACTION D_max: 174.6 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1xlt
沉积日期 deposition_date	2004-09-30
结构标题 title	Crystal structure of Transhydrogenase [(domain I)2:domain III] heterotrimer complex
关键词 keywords	Transhydrogenase, NAD, NADH, NADP, NADPH, 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	50.66 Å
回转半径 Rg (电子) rg_electron	50.67 Å
零角强度 I(0) i0	1218400000.00
分子量 molecular_weight	293120.0 kDa
排除体积 excluded_volume	368420 Å³
包络体积 envelope_volume	500850 Å³
水化壳体积 shell_volume	81670 Å³
包络直径 envelope_diameter	180.4 Å
壳层 Rg shell_rg	55.30 Å
包络 Rg envelope_rg	49.88 Å
形状 Rg shape_rg	50.67 Å
总 Rg total_rg	50.81 Å
总原子数 total_atoms	20480
残基数 n_residues	2700
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	174.6 Å
Rg (实空间) rg_real	50.69 Å
Rg 误差 (实空间) rg_real_error	1.77 Å
I(0) (实空间) i0_real	1.2180e+09
I(0) 误差 (实空间) i0_real_error	2.4840e+07
Rg (倒空间) rg_reciprocal	50.63 Å
I(0) (倒空间) i0_reciprocal	1218000000.0000
解质量估计 total_estimate	0.8735
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	62.0 Å
偏度 Skewness skewness	0.324
峰度 Kurtosis kurtosis	-0.331
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	89970000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.808

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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 (6)

Entity 1 polymer

描述 description	NAD(P) transhydrogenase subunit alpha part 1
分子量 formula_weight	40324.8 kDa
EC 编号 ec_number	1.6.1.2
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,D,E,G,H
原子数 atom_count	20480

MKIAIPKERRPGEDRVAISPEVVKKLVGLGFEVIVEQGAGVGASITDDALTAAGATIASTAAQALSQADVVWKVQRPMTAEEGTDEVALIKEGAVLMCHLGALTNRPVVEALTKRKITAYAMELMPRISRAQSMDILSSQSNLAGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGAVVMATDVRAATKEQVESLGGKFITVDDEAMKTAETAGGYAKEMGEEFRKKQAEAVLKELVKTDIAITTALIPGKPAPVLITEEMVTKMKPGSVIIDLAVEAGGNCPLSEPGKIVVKHGVKIVGHTNVPSRVAADASPLFAKNLLNFLTPHVDKDTKTLVMKLEDETVSGTCVTRDGAIVHPALTGQGA

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	18860.6 kDa
EC 编号 ec_number	1.6.1.2
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,F,I

RHMAGSAEDAAFIMKNASKVIIVPGYGMAVAQAQHALREMADVLKKEGVEVSYAIHPVAGRMPGHMNVLLAEANVPYDEVFELEEINSSFQTADVAFVIGANDVTNPAAKTDPSSPIYGMPILDVEKAGTVLFIKRSMASGYAGVENELFFRNNTMMLFGDAKKMTEQIVQAMN

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 3 branched

描述 description	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	man
拷贝数 entity_count	6

Entity 4 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	5

Entity 5 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 6 non-polymer

描述 description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
分子量 formula_weight	745.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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6. 折叠分类 (SCOP + CATH) 33 domains

SCOP 2.08 (18 domains)

结构域编号 domain_id	d1xlta1
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	d1xlta2
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	d1xltb1
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	d1xltb2
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	d1xltc2
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)

结构域编号 domain_id	d1xltc3
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	d1xltd1
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	d1xltd2
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	d1xlte1
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	d1xlte2
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	d1xltf2
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)

结构域编号 domain_id	d1xltf3
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	d1xltg1
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	d1xltg2
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	d1xlth1
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	d1xlth2
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	d1xlti2
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)

结构域编号 domain_id	d1xlti3
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 (15 domains)

结构域编号 domain_id	1xltA01
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	1xltA02
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	1xltB01
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	1xltB02
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	1xltC00
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

结构域编号 domain_id	1xltD01
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	1xltD02
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	1xltE01
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	1xltE02
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	1xltF00
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

结构域编号 domain_id	1xltG01
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	1xltG02
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	1xltH01
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	1xltH02
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	1xltI00
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

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7. 引用文献 (1)

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晶胞边长 a length_a	95.372 Å
晶胞边长 b length_b	171.082 Å
晶胞边长 c length_c	203.181 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	24

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	3.100 Å
最低分辨率 resolution_low	43.680 Å
R 因子 r_factor	—
R_work r_work	0.2320
R_free r_free	0.3100

fit	/app/data/saxs_computation/xl/1xlt/1xlt.fit
pddf	/app/data/pr_computation/xl/1xlt/1xlt.pr.out
profile	/app/data/saxs_computation/xl/1xlt/1xlt.dat

Crystal structure of Transhydrogenase [(domain I)2:domain III] heterotrimer 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

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 branched

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. 折叠分类 (SCOP + CATH) 33 domains

SCOP 2.08 (18 domains)

CATH v4.4 (15 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)