SAXSdb — 2iu9

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2iu9
沉积日期 deposition_date	2006-05-30
结构标题 title	Chlamydia trachomatis LpxD with 100mM UDPGlcNAc (Complex II)
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	31.70 Å
回转半径 Rg (电子) rg_electron	31.07 Å
零角强度 I(0) i0	207810000.00
分子量 molecular_weight	114970.0 kDa
排除体积 excluded_volume	143970 Å³
包络体积 envelope_volume	179240 Å³
水化壳体积 shell_volume	47068 Å³
包络直径 envelope_diameter	108.3 Å
壳层 Rg shell_rg	38.79 Å
包络 Rg envelope_rg	31.80 Å
形状 Rg shape_rg	31.09 Å
总 Rg total_rg	31.62 Å
总原子数 total_atoms	8077
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	102.3 Å
Rg (实空间) rg_real	31.58 Å
Rg 误差 (实空间) rg_real_error	0.64 Å
I(0) (实空间) i0_real	2.0780e+08
I(0) 误差 (实空间) i0_real_error	2.9140e+06
Rg (倒空间) rg_reciprocal	31.63 Å
I(0) (倒空间) i0_reciprocal	207800000.0000
解质量估计 total_estimate	0.8950
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	0.254
峰度 Kurtosis kurtosis	-0.413
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	52320000.0000
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: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.979

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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 (6)

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	8271

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

Entity 3 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 4 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 5 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	2

Entity 6 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	99

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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	2iu9A01
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	2iu9A02
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	2iu9B01
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	2iu9B02
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	2iu9C01
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	2iu9C02
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	2iu9C03
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	98.871 Å
晶胞边长 b length_b	98.872 Å
晶胞边长 c length_c	283.053 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	3.100 Å
最低分辨率 resolution_low	28.500 Å
R 因子 r_factor	0.2240
R_work r_work	0.2210
R_free r_free	0.2810

fit	/app/data/saxs_computation/iu/2iu9/2iu9.fit
pddf	/app/data/pr_computation/iu/2iu9/2iu9.pr.out
profile	/app/data/saxs_computation/iu/2iu9/2iu9.dat

Chlamydia trachomatis LpxD with 100mM UDPGlcNAc (Complex II)

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