2aaz

Cryptococcus neoformans thymidylate synthase complexed with substrate and an antifolate

Method: X-RAY DIFFRACTION D_max: 257.8 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	2aaz
沉积日期 deposition_date	2005-07-14
结构标题 title	Cryptococcus neoformans thymidylate synthase complexed with substrate and an antifolate
关键词 keywords	Methyl transferase, Nucleotide biosynthesis, Transferase; TRANSFERASE
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	80.65 Å
回转半径 Rg (电子) rg_electron	81.89 Å
零角强度 I(0) i0	4224090000.00
分子量 molecular_weight	555380.0 kDa
排除体积 excluded_volume	696680 Å³
包络体积 envelope_volume	1122100 Å³
水化壳体积 shell_volume	127360 Å³
包络直径 envelope_diameter	297.4 Å
壳层 Rg shell_rg	66.90 Å
包络 Rg envelope_rg	79.99 Å
形状 Rg shape_rg	81.89 Å
总 Rg total_rg	81.66 Å
总原子数 total_atoms	39136
残基数 n_residues	4832
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	257.8 Å
Rg (实空间) rg_real	80.86 Å
Rg 误差 (实空间) rg_real_error	2.02 Å
I(0) (实空间) i0_real	4.2110e+09
I(0) 误差 (实空间) i0_real_error	8.0380e+07
Rg (倒空间) rg_reciprocal	77.39 Å
I(0) (倒空间) i0_reciprocal	4187000000.0000
解质量估计 total_estimate	0.8803
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	95.0 Å
偏度 Skewness skewness	0.650
峰度 Kurtosis kurtosis	0.115
角度范围 angular_range	— – 0.0950 Å⁻¹
当前正则化参数 α current_alpha	0.0144
最高正则化参数 α highest_alpha	60010000.0000
实空间数据点数 n_real_points	20
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.955

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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	Thymidylate synthase
分子量 formula_weight	35912.0 kDa
EC 编号 ec_number	2.1.1.45
来源方法 src_method	man
拷贝数 entity_count	16

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
原子数 atom_count	161392

MTATIDDQEKNQRSNPDHEEYQYLDLIRRIINVGEVRPDRTGTGTVALFAPPSFRFSLADNTLPLLTTKRVFLRGVIAELLWFVSGCTDAKMLSSQGVGIWDGNGSKEFLEKVGLGHRREGDLGPVYGFQWRHFGAEYTDADGDYKGKGVDQLQRVIDTIKNNPTDRRIILSAWNPKDLPLMALPPCHMFCQFFVSLPPADSPGSKPKLSCLMYQRSCDLGLGVPFNIASYALLTHMIALITDTEPHEFILQMGDAHVYRDHVEPLKTQLEREPRDFPKLKWARSKEEIGDIDGFKVEDFVVEGYKPWGKIDMKMSA

来源 Source

来源生物 organism	Filobasidiella neoformans
NCBI 分类编号 ncbi_taxonomy_id	5207
宿主生物 host_organism	Escherichia coli BL21

Entity 2 non-polymer

描述 description	;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ;
分子量 formula_weight	308.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	16

Entity 3 non-polymer

描述 description	10-PROPARGYL-5,8-DIDEAZAFOLIC ACID
分子量 formula_weight	477.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	1212

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6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

结构域编号 domain_id	d2aaza_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aazb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aazc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aazd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aaze_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aazf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aazg_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aazh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aazi_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aazj_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aazk_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aazl_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aazm_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aazn_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aazo_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d2aazp_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

CATH v4.4 (16 domains)

结构域编号 domain_id	2aazA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazJ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazK00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazL00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazM00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazN00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazO00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	2aazP00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

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7. 引用文献 (3)

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晶胞边长 a length_a	179.400 Å
晶胞边长 b length_b	179.500 Å
晶胞边长 c length_c	209.100 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	89.80 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	64

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.080 Å
最低分辨率 resolution_low	49.910 Å
R 因子 r_factor	0.2900
R_work r_work	0.2900
R_free r_free	0.3050

fit	/app/data/saxs_computation/aa/2aaz/2aaz.fit
pddf	/app/data/pr_computation/aa/2aaz/2aaz.pr.out
profile	/app/data/saxs_computation/aa/2aaz/2aaz.dat