SAXSdb — 1jol

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jol
沉积日期 deposition_date	1996-02-25
结构标题 title	THE CRYSTAL STRUCTURE OF THE BINARY COMPLEX BETWEEN FOLINIC ACID (LEUCOVORIN) AND E. COLI DIHYDROFOLATE REDUCTASE
关键词 keywords	METHOTREXATE RESISTANCE, ONE-CARBON METABOLISM, 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	23.24 Å
回转半径 Rg (电子) rg_electron	22.63 Å
零角强度 I(0) i0	23624700.00
分子量 molecular_weight	36590.0 kDa
排除体积 excluded_volume	45467 Å³
包络体积 envelope_volume	54581 Å³
水化壳体积 shell_volume	20904 Å³
包络直径 envelope_diameter	75.4 Å
壳层 Rg shell_rg	28.60 Å
包络 Rg envelope_rg	22.51 Å
形状 Rg shape_rg	22.60 Å
总 Rg total_rg	23.48 Å
总原子数 total_atoms	2577
残基数 n_residues	318
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	75.4 Å
Rg (实空间) rg_real	23.29 Å
Rg 误差 (实空间) rg_real_error	0.42 Å
I(0) (实空间) i0_real	2.3620e+07
I(0) 误差 (实空间) i0_real_error	3.1480e+05
Rg (倒空间) rg_reciprocal	23.28 Å
I(0) (倒空间) i0_reciprocal	23620000.0000
解质量估计 total_estimate	0.8895
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	24.4 Å
偏度 Skewness skewness	0.396
峰度 Kurtosis kurtosis	-0.421
角度范围 angular_range	— – 0.3400 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	5849000.0000
实空间数据点数 n_real_points	66
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.977

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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 (5)

Entity 1 polymer

描述 description	DIHYDROFOLATE REDUCTASE
分子量 formula_weight	18020.3 kDa
EC 编号 ec_number	1.5.1.3
来源方法 src_method	nat
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	3004

MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLDKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR

Entity 2 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid
分子量 formula_weight	473.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	427

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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	d1jola_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.71 — Dihydrofolate reductase-like
超家族 Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
家族 Family family	c.71.1.1 — Dihydrofolate reductases

结构域编号 domain_id	d1jolb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.71 — Dihydrofolate reductase-like
超家族 Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
家族 Family family	c.71.1.1 — Dihydrofolate reductases

CATH v4.4 (2 domains)

结构域编号 domain_id	1jolA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	430 — Dihydrofolate Reductase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

结构域编号 domain_id	1jolB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	430 — Dihydrofolate Reductase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

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7. 引用文献 (7)

;Crystal structures of Escherichia coli dihydrofolate reductase complexed with 5-formyltetrahydrofolate (folinic acid) in two space groups: evidence for enolization of pteridine O4. ;

Biochemistry (1996)

PMID: 8679526 · DOI: 10.1021/bi960028g PRIMARY

;Isomorphous Crystal Structures of Escherichia Coli Dihydrofolate Reductase Complexed with Folate, 5-Deazafolate, and 5,10-Dideazatetrahydrofolate: Mechanistic Implications ;

Biochemistry (1995)

;Crystal Structure of Unliganded Escherichia Coli Dihydrofolate Reductase. Ligand-Induced Conformational Changes and Cooperativity in Binding ;

Biochemistry (1991)

Crystal Structures of Recombinant Human Dihydrofolate Reductase Complexed with Folate and 5-Deazafolate

Biochemistry (1990)

;Crystal Structures of Escherichia Coli Dihydrofolate Reductase: The Nadp+ Holoenzyme and the Folate.Nadp+ Ternary Complex. Substrate Binding and a Model for the Transition State ;

Biochemistry (1990)

;Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 A Resolution. II. Environment of Bound Nadph and Implications for Catalysis ;

J.Biol.Chem. (1982)

;Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 A Resolution. I. General Features and Binding of Methotrexate ;

J.Biol.Chem. (1982)

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晶胞边长 a length_a	92.577 Å
晶胞边长 b length_b	92.577 Å
晶胞边长 c length_c	73.132 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 61
空间群编号 int_tables_number	169
晶系 crystal_system	—

分辨率 resolution	1.960 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	0.1420
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/jo/1jol/1jol.fit
pddf	/app/data/pr_computation/jo/1jol/1jol.pr.out
profile	/app/data/saxs_computation/jo/1jol/1jol.dat

THE CRYSTAL STRUCTURE OF THE BINARY COMPLEX BETWEEN FOLINIC ACID (LEUCOVORIN) AND E. COLI DIHYDROFOLATE REDUCTASE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution