1iyl

Crystal Structure of Candida albicans N-myristoyltransferase with Non-peptidic Inhibitor

Method: X-RAY DIFFRACTION D_max: 166.6 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	1iyl
沉积日期 deposition_date	2002-08-29
结构标题 title	Crystal Structure of Candida albicans N-myristoyltransferase with Non-peptidic Inhibitor
关键词 keywords	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	51.34 Å
回转半径 Rg (电子) rg_electron	51.29 Å
零角强度 I(0) i0	423657000.00
分子量 molecular_weight	177930.0 kDa
排除体积 excluded_volume	225600 Å³
包络体积 envelope_volume	321490 Å³
水化壳体积 shell_volume	56964 Å³
包络直径 envelope_diameter	179.3 Å
壳层 Rg shell_rg	49.26 Å
包络 Rg envelope_rg	49.47 Å
形状 Rg shape_rg	51.26 Å
总 Rg total_rg	51.30 Å
总原子数 total_atoms	12597
残基数 n_residues	1525
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	166.6 Å
Rg (实空间) rg_real	51.59 Å
Rg 误差 (实空间) rg_real_error	2.06 Å
I(0) (实空间) i0_real	4.2370e+08
I(0) 误差 (实空间) i0_real_error	9.5300e+06
Rg (倒空间) rg_reciprocal	51.12 Å
I(0) (倒空间) i0_reciprocal	423400000.0000
解质量估计 total_estimate	0.7941
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	69.9 Å
偏度 Skewness skewness	0.419
峰度 Kurtosis kurtosis	-0.307
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35440000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.842; Smooth: 0.082

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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 (2)

Entity 1 polymer

描述 description	Myristoyl-CoA:Protein N-Myristoyltransferase
分子量 formula_weight	45421.6 kDa
EC 编号 ec_number	2.3.1.97
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	12597

EGPIDKLKTPEDVPNDPLPLISDFEWSTLDIDDNLQLDELYKLLYDNYVEDIDATFRFKYSHEFFQWALKPPGWRKDWHVGVRVKSTGKLVAFIAATPVTFKLNKSNKVIDSVEINFLCIHKKLRNKRLAPVLIKEITRRVNKQNIWQALYTGGSILPTPLTTCRYQHRPINWSKLHDVGFSHLPPNQTKSSMVASYTLPNNPKLKGLRPMTGKDVSTVLSLLYKYQERFDIVQLFTEEEFKHWMLGHDENSDSNVVKSYVVEDENGIITDYFSYYLLPFTVLDNAQHDELGIAYLFYYASDSFEKPNYKKRLNELITDALITSKKFGVDVFNCLTCQDNTYFLKDCKFGSGDGFLNYYLFNYRTFPMDGGIDKKTKEVVEDQTSGIGVVLL

来源 Source

来源生物 organism	Candida albicans
NCBI 分类编号 ncbi_taxonomy_id	5476
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	(1-METHYL-1H-IMIDAZOL-2-YL)-(3-METHYL-4-{3-[(PYRIDIN-3-YLMETHYL)-AMINO]-PROPOXY}-BENZOFURAN-2-YL)-METHANONE
分子量 formula_weight	404.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1iyla1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
超家族 Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
家族 Family family	d.108.1.2 — N-myristoyl transferase, NMT

结构域编号 domain_id	d1iyla2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
超家族 Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
家族 Family family	d.108.1.2 — N-myristoyl transferase, NMT

结构域编号 domain_id	d1iylb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
超家族 Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
家族 Family family	d.108.1.2 — N-myristoyl transferase, NMT

结构域编号 domain_id	d1iylb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
超家族 Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
家族 Family family	d.108.1.2 — N-myristoyl transferase, NMT

结构域编号 domain_id	d1iylc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
超家族 Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
家族 Family family	d.108.1.2 — N-myristoyl transferase, NMT

结构域编号 domain_id	d1iylc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
超家族 Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
家族 Family family	d.108.1.2 — N-myristoyl transferase, NMT

结构域编号 domain_id	d1iyld1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
超家族 Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
家族 Family family	d.108.1.2 — N-myristoyl transferase, NMT

结构域编号 domain_id	d1iyld2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
超家族 Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
家族 Family family	d.108.1.2 — N-myristoyl transferase, NMT

CATH v4.4 (8 domains)

结构域编号 domain_id	1iylA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

结构域编号 domain_id	1iylA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

结构域编号 domain_id	1iylB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

结构域编号 domain_id	1iylB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

结构域编号 domain_id	1iylC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

结构域编号 domain_id	1iylC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

结构域编号 domain_id	1iylD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

结构域编号 domain_id	1iylD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

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7. 引用文献 (1)

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晶胞边长 a length_a	93.277 Å
晶胞边长 b length_b	96.885 Å
晶胞边长 c length_c	269.277 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	3.200 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.2880
R_work r_work	0.2840
R_free r_free	0.3660

fit	/app/data/saxs_computation/iy/1iyl/1iyl.fit
pddf	/app/data/pr_computation/iy/1iyl/1iyl.pr.out
profile	/app/data/saxs_computation/iy/1iyl/1iyl.dat

Crystal Structure of Candida albicans N-myristoyltransferase with Non-peptidic Inhibitor

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