SAXSdb — 1i0z

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1i0z
沉积日期 deposition_date	2001-01-30
结构标题 title	HUMAN HEART L-LACTATE DEHYDROGENASE H CHAIN, TERNARY COMPLEX WITH NADH AND OXAMATE
关键词 keywords	DEHYDROGENASE, ROSSMANN FOLD, 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	27.57 Å
回转半径 Rg (电子) rg_electron	26.71 Å
零角强度 I(0) i0	87510100.00
分子量 molecular_weight	74251.0 kDa
排除体积 excluded_volume	93435 Å³
包络体积 envelope_volume	112090 Å³
水化壳体积 shell_volume	34266 Å³
包络直径 envelope_diameter	91.8 Å
壳层 Rg shell_rg	34.69 Å
包络 Rg envelope_rg	27.16 Å
形状 Rg shape_rg	26.73 Å
总 Rg total_rg	27.45 Å
总原子数 total_atoms	5204
残基数 n_residues	664
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	88.8 Å
Rg (实空间) rg_real	27.54 Å
Rg 误差 (实空间) rg_real_error	0.53 Å
I(0) (实空间) i0_real	8.7510e+07
I(0) 误差 (实空间) i0_real_error	1.2910e+06
Rg (倒空间) rg_reciprocal	27.55 Å
I(0) (倒空间) i0_reciprocal	87510000.0000
解质量估计 total_estimate	0.7260
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	30.6 Å
偏度 Skewness skewness	0.339
峰度 Kurtosis kurtosis	-0.387
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	25550000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 0.267; Positv: 1.000; Valcen: 1.000; Smooth: 0.960

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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 (4)

Entity 1 polymer

描述 description	L-LACTATE DEHYDROGENASE H CHAIN
分子量 formula_weight	36548.2 kDa
EC 编号 ec_number	1.1.1.27
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	5522

ATLKEKLIAPVAEEEATVPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVKGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSADTLWDIQKDLKDL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

Entity 2 non-polymer

描述 description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
分子量 formula_weight	665.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	OXAMIC ACID
分子量 formula_weight	89.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	318

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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	d1i0za1
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.2.1.5 — LDH N-terminal domain-like

结构域编号 domain_id	d1i0za2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.162 — LDH C-terminal domain-like
超家族 Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
家族 Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

结构域编号 domain_id	d1i0zb1
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.2.1.5 — LDH N-terminal domain-like

结构域编号 domain_id	d1i0zb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.162 — LDH C-terminal domain-like
超家族 Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
家族 Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1i0zA01
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	1i0zA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

结构域编号 domain_id	1i0zB01
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	1i0zB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

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7. 引用文献 (1)

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晶胞边长 a length_a	59.491 Å
晶胞边长 b length_b	161.683 Å
晶胞边长 c length_c	137.846 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	16

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1795
R_work r_work	0.1768
R_free r_free	0.2301

fit	/app/data/saxs_computation/i0/1i0z/1i0z.fit
pddf	/app/data/pr_computation/i0/1i0z/1i0z.pr.out
profile	/app/data/saxs_computation/i0/1i0z/1i0z.dat

HUMAN HEART L-LACTATE DEHYDROGENASE H CHAIN, TERNARY COMPLEX WITH NADH AND OXAMATE

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