SAXSdb — 1j3n

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1j3n
沉积日期 deposition_date	2003-02-10
结构标题 title	Crystal Structure of 3-oxoacyl-(acyl-carrier protein) Synthase II from Thermus thermophilus HB8
关键词 keywords	;Condensing Enzymes, Fatty acid elongation, Acyl-carrier protein (ACP), Beta-keto-ACP synthase (KAS), Homodimer, Structural genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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	26.40 Å
回转半径 Rg (电子) rg_electron	25.28 Å
零角强度 I(0) i0	120943000.00
分子量 molecular_weight	86626.0 kDa
排除体积 excluded_volume	108470 Å³
包络体积 envelope_volume	121490 Å³
水化壳体积 shell_volume	38010 Å³
包络直径 envelope_diameter	82.1 Å
壳层 Rg shell_rg	34.38 Å
包络 Rg envelope_rg	25.48 Å
形状 Rg shape_rg	25.29 Å
总 Rg total_rg	26.13 Å
总原子数 total_atoms	6092
残基数 n_residues	816
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	80.6 Å
Rg (实空间) rg_real	26.25 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	1.2090e+08
I(0) 误差 (实空间) i0_real_error	1.8260e+06
Rg (倒空间) rg_reciprocal	26.30 Å
I(0) (倒空间) i0_reciprocal	120900000.0000
解质量估计 total_estimate	0.9032
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	32.2 Å
偏度 Skewness skewness	0.202
峰度 Kurtosis kurtosis	-0.413
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	41970000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.992

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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	3-oxoacyl-(acyl-carrier protein) synthase II
分子量 formula_weight	43262.5 kDa
EC 编号 ec_number	2.3.1.41
来源方法 src_method	man
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	6556

MRRVVVTGLGALTPIGVGQEAFHKAQLAGKSGVRPITRFDASALPVRIAAEVDVDPGAYLDRKELRRLDRFVQYALIAAQLALEDAGLKPEDLDPERVGTLVGTGIGGMETWEAQSRVFLERGPNRISPFFIPMMIANMASAHIAMRYGFTGPSSTVVTACATGADALGSALRMIQLGEADLVLAGGTEAAITPMAIGAFAVMRALSTRNEEPEKASRPFTLSRDGFVMGEGAGVLVLEAYEHAKKRGARIYAELVGFGRSADAHHITEPHPEGKGAALAMARALKDAGIAPEQVGYINAHGTSTPVGDRAEVLAIKRVFGDHAKRLMVSSTKSMIGHLLGAAGAVEAIATVQALYHGVIPPTINLEDPDPELDLDFVPEPREAKVDYALSNSFAFGGHNAVLAFKRV

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	CITRIC ACID
分子量 formula_weight	192.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	462

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1j3na1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.95 — Thiolase-like
超家族 Superfamily superfamily	c.95.1 — Thiolase-like
家族 Family family	c.95.1.1 — Thiolase-related

结构域编号 domain_id	d1j3na2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.95 — Thiolase-like
超家族 Superfamily superfamily	c.95.1 — Thiolase-like
家族 Family family	c.95.1.1 — Thiolase-related

结构域编号 domain_id	d1j3nb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.95 — Thiolase-like
超家族 Superfamily superfamily	c.95.1 — Thiolase-like
家族 Family family	c.95.1.1 — Thiolase-related

结构域编号 domain_id	d1j3nb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.95 — Thiolase-like
超家族 Superfamily superfamily	c.95.1 — Thiolase-like
家族 Family family	c.95.1.1 — Thiolase-related

CATH v4.4 (4 domains)

结构域编号 domain_id	1j3nA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

结构域编号 domain_id	1j3nA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

结构域编号 domain_id	1j3nB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

结构域编号 domain_id	1j3nB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

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7. 引用文献 (1)

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晶胞边长 a length_a	72.067 Å
晶胞边长 b length_b	185.573 Å
晶胞边长 c length_c	62.517 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	8

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.2100
R_free r_free	0.2576

fit	/app/data/saxs_computation/j3/1j3n/1j3n.fit
pddf	/app/data/pr_computation/j3/1j3n/1j3n.pr.out
profile	/app/data/saxs_computation/j3/1j3n/1j3n.dat

Crystal Structure of 3-oxoacyl-(acyl-carrier protein) Synthase II from Thermus thermophilus HB8

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