SAXSdb — 2iu8

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2iu8
沉积日期 deposition_date	2006-05-30
结构标题 title	Chlamydia trachomatis LpxD with 25mM UDPGlcNAc (Complex I)
关键词 keywords	;TRANSFERASE, UDP-3- O-ACYL-GLUCOSAMINE N-ACYLTRANSFERASE, ACYLTRANSFERASE, LIPID A BIOSYNTHESIS, LEFT-HANDED BETA HELIX, COMPLEX WITH UDPGLCNAC, ENZYME, HOMOTRIMER, LIPID SYNTHESIS ;; 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	31.73 Å
回转半径 Rg (电子) rg_electron	31.10 Å
零角强度 I(0) i0	204821000.00
分子量 molecular_weight	114430.0 kDa
排除体积 excluded_volume	143450 Å³
包络体积 envelope_volume	179330 Å³
水化壳体积 shell_volume	47047 Å³
包络直径 envelope_diameter	108.5 Å
壳层 Rg shell_rg	38.73 Å
包络 Rg envelope_rg	31.85 Å
形状 Rg shape_rg	31.12 Å
总 Rg total_rg	31.66 Å
总原子数 total_atoms	8042
残基数 n_residues	1037
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	102.4 Å
Rg (实空间) rg_real	31.62 Å
Rg 误差 (实空间) rg_real_error	0.69 Å
I(0) (实空间) i0_real	2.0480e+08
I(0) 误差 (实空间) i0_real_error	3.2810e+06
Rg (倒空间) rg_reciprocal	31.67 Å
I(0) (倒空间) i0_reciprocal	204800000.0000
解质量估计 total_estimate	0.8946
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	38.9 Å
偏度 Skewness skewness	0.255
峰度 Kurtosis kurtosis	-0.409
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	49260000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.976

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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 (7)

Entity 1 polymer

描述 description	UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE
分子量 formula_weight	40629.3 kDa
EC 编号 ec_number	2.3.1.-
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	8688

MGSSHHHHHHSSGLVPRGSHMSQSTYSLEQLADFLKVEFQGNGATLLSGVEEIEEAKTAHITFLDNEKYAKHLKSSEAGAIIISRTQFQKYRDLNKNFLITSESPSLVFQKCLELFITPVDSGFPGIHPTAVIHPTAIIEDHVCIEPYAVVCQHAHVGSACHIGSGSVIGAYSTVGEHSYIHPRVVIRERVSIGKRVIIQPGAVIGSCGFGYVTSAFGQHKHLKHLGKVIIEDDVEIGANTTIDRGRFKHSVVREGSKIDNLVQIAHQVEVGQHSMIVAQAGIAGSTKIGNHVIIGGQAGITGHICIADHVIMMAQTGVTKSITSPGIYGGAPARPYQEIHRQVAKVRNLPRLEERIAALEKLVQKLEALSEQH

来源 Source

来源生物 organism	CHLAMYDIA TRACHOMATIS
NCBI 分类编号 ncbi_taxonomy_id	813
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 3 non-polymer

描述 description	PALMITIC ACID
分子量 formula_weight	256.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 4 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	BETA-MERCAPTOETHANOL
分子量 formula_weight	78.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
分子量 formula_weight	607.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 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	495

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6. 折叠分类 (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

结构域编号 domain_id	2iu8A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — MurE/MurF, N-terminal domain

结构域编号 domain_id	2iu8A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	160 — 3 Solenoid
拓扑 Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Hexapeptide repeat proteins

结构域编号 domain_id	2iu8B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — MurE/MurF, N-terminal domain

结构域编号 domain_id	2iu8B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	160 — 3 Solenoid
拓扑 Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Hexapeptide repeat proteins

结构域编号 domain_id	2iu8C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — MurE/MurF, N-terminal domain

结构域编号 domain_id	2iu8C02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	160 — 3 Solenoid
拓扑 Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Hexapeptide repeat proteins

结构域编号 domain_id	2iu8C03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	170 —

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7. 引用文献 (1)

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晶胞边长 a length_a	98.805 Å
晶胞边长 b length_b	98.805 Å
晶胞边长 c length_c	283.082 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	24

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2090
R_work r_work	0.2060
R_free r_free	0.2560

fit	/app/data/saxs_computation/iu/2iu8/2iu8.fit
pddf	/app/data/pr_computation/iu/2iu8/2iu8.pr.out
profile	/app/data/saxs_computation/iu/2iu8/2iu8.dat

Chlamydia trachomatis LpxD with 25mM UDPGlcNAc (Complex I)

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution