SAXSdb — 1gpd

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gpd
沉积日期 deposition_date	1975-07-01
结构标题 title	STUDIES OF ASYMMETRY IN THE THREE-DIMENSIONAL STRUCTURE OF LOBSTER D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
关键词 keywords	OXIDO-REDUCTASE(ALDEHYDE/DONR, NAD/ACCPT), OXIDO-REDUCTASE(ALDEHYDE-DONR, NAD-ACCPT) COMPLEX, 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	29.64 Å
回转半径 Rg (电子) rg_electron	29.36 Å
零角强度 I(0) i0	86316100.00
分子量 molecular_weight	72967.0 kDa
排除体积 excluded_volume	91287 Å³
包络体积 envelope_volume	112270 Å³
水化壳体积 shell_volume	32544 Å³
包络直径 envelope_diameter	96.5 Å
壳层 Rg shell_rg	35.89 Å
包络 Rg envelope_rg	29.12 Å
形状 Rg shape_rg	29.34 Å
总 Rg total_rg	30.02 Å
总原子数 total_atoms	5112
残基数 n_residues	666
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	95.6 Å
Rg (实空间) rg_real	29.66 Å
Rg 误差 (实空间) rg_real_error	0.61 Å
I(0) (实空间) i0_real	8.6320e+07
I(0) 误差 (实空间) i0_real_error	1.2530e+06
Rg (倒空间) rg_reciprocal	29.66 Å
I(0) (倒空间) i0_reciprocal	86320000.0000
解质量估计 total_estimate	0.8984
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	28.9 Å
偏度 Skewness skewness	0.297
峰度 Kurtosis kurtosis	-0.599
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	30740000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.953

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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 (3)

Entity 1 polymer

描述 description	D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
分子量 formula_weight	35783.9 kDa
EC 编号 ec_number	1.2.1.12
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	G,R
原子数 atom_count	5112

XSKIGINGFGRIGRLVLRAALSCGAQVVAVNDPFIALEYMVYMFKYDSTHGVFKGEVKMEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTTIEKASAHFKGGAKKVVISAPSADAPMFVCGVNLEKYSKDMTVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQNIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPDVSVVDLTVRLGKECSYDDIKAAMKTASEGPLQGFLGYTEDDVVSSDFIGDNRSSIFDAKAGIQLSKTFVKVVSWYDNEFGYSQRVIDLLKHMQKVDSA

来源 Source

来源生物 organism	Homarus americanus
通用名 common_name	American lobster
NCBI 分类编号 ncbi_taxonomy_id	6706

Entity 2 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	2

Entity 3 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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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	d1gpdg1
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.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1gpdg2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.1 — GAPDH-like

结构域编号 domain_id	d1gpdr1
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.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1gpdr2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.1 — GAPDH-like

CATH v4.4 (4 domains)

结构域编号 domain_id	1gpdG01
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	1gpdG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	1gpdR01
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	1gpdR02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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7. 引用文献 (11)

Studies of asymmetry in the three-dimensional structure of lobster D-glyceraldehyde-3-phosphate dehydrogenase.

J.Biol.Chem. (1975)

PMID: 127793 PRIMARY

Anion Binding Sites in the Active Center of D-Glyceraldehyde-3-Phosphate Dehydrogenase

J.Mol.Biol. (1976)

无标题

Atlas of Protein Sequence and Structure,Supplement 2 (1976)

Studies on Coenzyme Binding to Glyceraldehyde-3-Phosphate Dehydrogenase

J.Mol.Biol. (1976)

无标题

Atlas of Macromolecular Structure on Microfiche (1976)

A Comparison of the Binding and Function of Nad with Respect to Lactate Dehydrogenase and Glyceraldehyde-3-Phosphate Dehydrogenase

;STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN ; (1975)

Sequence Variability and Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase

J.Biol.Chem. (1975)

An Application of the Molecular Replacement Technique in Direct Space to a Known Protein Structure

Acta Crystallogr.,Sect.A (1975)

Three-Dimensional Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase

J.Mol.Biol. (1974)

Structure Determination of Crystalline Lobster D-Glyceraldehyde-3-Phosphate Dehydrogenase

J.Mol.Biol. (1974)

D-Glyceraldehyde-3-Phosphate Dehydrogenase,Three Dimensional Structure and Evolutionary Significance

Proc.Natl.Acad.Sci.USA (1973)

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晶胞边长 a length_a	149.000 Å
晶胞边长 b length_b	139.100 Å
晶胞边长 c length_c	80.700 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	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/gp/1gpd/1gpd.fit
pddf	/app/data/pr_computation/gp/1gpd/1gpd.pr.out
profile	/app/data/saxs_computation/gp/1gpd/1gpd.dat

STUDIES OF ASYMMETRY IN THE THREE-DIMENSIONAL STRUCTURE OF LOBSTER D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution