SAXSdb — 1ldm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ldm
沉积日期 deposition_date	1987-11-25
结构标题 title	Refined crystal structure of dogfish M4 apo-lactate dehydrogenase
关键词 keywords	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	21.90 Å
回转半径 Rg (电子) rg_electron	21.27 Å
零角强度 I(0) i0	23581100.00
分子量 molecular_weight	37106.0 kDa
排除体积 excluded_volume	46598 Å³
包络体积 envelope_volume	57372 Å³
水化壳体积 shell_volume	22695 Å³
包络直径 envelope_diameter	86.9 Å
壳层 Rg shell_rg	27.90 Å
包络 Rg envelope_rg	22.72 Å
形状 Rg shape_rg	21.27 Å
总 Rg total_rg	22.15 Å
总原子数 total_atoms	2598
残基数 n_residues	329
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	83.7 Å
Rg (实空间) rg_real	22.03 Å
Rg 误差 (实空间) rg_real_error	0.67 Å
I(0) (实空间) i0_real	2.3580e+07
I(0) 误差 (实空间) i0_real_error	3.4830e+05
Rg (倒空间) rg_reciprocal	22.01 Å
I(0) (倒空间) i0_reciprocal	23580000.0000
解质量估计 total_estimate	0.7760
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	25.0 Å
偏度 Skewness skewness	0.665
峰度 Kurtosis kurtosis	0.587
角度范围 angular_range	— – 0.3650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6104000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.463; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.770; Smooth: 0.924

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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	M4 LACTATE DEHYDROGENASE
分子量 formula_weight	36327.3 kDa
EC 编号 ec_number	1.1.1.27
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	2843

ATLKDKLIGHLATSQEPRSYNKITVVGVGAVGMACAISILMKDLADEVALVDVMEDKLKGEMMDLQHGSLFLHTAKIVSGKDYSVSAGSKLVVITAGARQQEGESRLNLVQRNVNIFKFIIPNIVKHSPDCIILVVSNPVDVLTYVAWKLSGLPMHRIIGSGCNLDSARFRYLMGERLGVHSCSCHGWVIGEHGDSVPSVWSGMNVASIKLHPLDGTNKDKQDWKKLHKDVVDSAYEVIKLKGYTSWAIGLSVADLAETIMKNLCRVHPVSTMVKDFYGIKDNVFLSLPCVLNDHGISNIVKMKLKPNEEQQLQKSATTLWDIQKDLKF

来源 Source

来源生物 organism	Squalus acanthias
通用名 common_name	spiny dogfish
NCBI 分类编号 ncbi_taxonomy_id	7797

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	1

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	245

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1ldma1
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	d1ldma2
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 (2 domains)

结构域编号 domain_id	1ldmA01
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	1ldmA02
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 (20)

Refined crystal structure of dogfish M4 apo-lactate dehydrogenase.

J.Mol.Biol. (1987)

PMID: 3430615 · DOI: 10.1016/0022-2836(87)90293-2 PRIMARY

Structural Adaptations of Lactate Dehydrogenase Isozymes

Proc.Natl.Acad.Sci.USA (1977)

A Comparison of the Structures of Apo Dogfish M4 Lactate Dehydrogenase and its Ternary Complexes

J.Mol.Biol. (1976)

A 5 Angstroms X-Ray Diffraction Study of Coenzyme-Deficient Lactate Dehydrogenase,Nad-Pyruvate Ternary Complex

J.Mol.Biol. (1975)

A Structural Comparison of Porcine B4 and Dogfish A4 Isozymes of Lactate Dehydrogenase

Isozymes-Molecular Structure (1975)

Lactate Dehydrogenase

The Enzymes,Third Edition (1975)

X-Ray Studies of Protein Interactions

Annu.Rev.Biochem. (1974)

Chemical and Biological Evolution of a Nucleotide Binding Protein

Nature (1974)

Recognition of Structural Domains in Globular Proteins

J.Mol.Biol. (1974)

Structure-Function Relationships in Lactate Dehydrogenase

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

Amino-Acid Sequence of Dogfish M4 Lactate Dehydrogenase

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

Molecular Symmetry Axes and Subunit Interfaces in Certain Dehydrogenases

J.Mol.Biol. (1973)

Functional Anion Binding Sites in Dogfish M4 Lactate Dehydrogenase

J.Mol.Biol. (1973)

Binding of Oxamate to the Apoenzyme of Dogfish M4 Lactate Dehydrogenase

J.Mol.Biol. (1973)

Conformation of Coenzyme Fragments When Bound to Lactate Dehydrogenase

J.Mol.Biol. (1973)

Atomic Co-Ordinates for Dogfish M4 Apo-Lactate Dehydrogenase

Biochem.Biophys.Res.Commun. (1973)

The 5 Angstroms Resolution Structure of an Abortive Ternary Complex of Lactate Dehydrogenase and its Comparison with the Apo-Enzyme

J.Mol.Biol. (1971)

Structure of Lactate Dehydrogenase at 2.8 Angstroms Resolution

Nature (1970)

Low Resolution Study of Crystalline L-Lactate Dehydrogenase

J.Mol.Biol. (1969)

The Crystal Structure of Lactic Dehydrogenase

Proc.Natl.Acad.Sci.USA (1967)

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晶胞边长 a length_a	134.500 Å
晶胞边长 b length_b	134.500 Å
晶胞边长 c length_c	85.900 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 4 21 2
空间群编号 int_tables_number	90
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	6.000 Å
R 因子 r_factor	0.1730
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/ld/1ldm/1ldm.fit
pddf	/app/data/pr_computation/ld/1ldm/1ldm.pr.out
profile	/app/data/saxs_computation/ld/1ldm/1ldm.dat

Refined crystal structure of dogfish M4 apo-lactate dehydrogenase

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. 引用文献 (20)

8. 文件与曲线 (10)

Files (7)

Curves (3)