SAXSdb — 1f8m

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1f8m
沉积日期 deposition_date	2000-06-30
结构标题 title	CRYSTAL STRUCTURE OF 3-BROMOPYRUVATE MODIFIED ISOCITRATE LYASE (ICL) FROM MYCOBACTERIUM TUBERCULOSIS
关键词 keywords	;Alpha-beta barrel, Helix-swapping, closed conformation, bromopyuvate modification, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, LYASE ;; LYASE
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	33.39 Å
回转半径 Rg (电子) rg_electron	32.35 Å
零角强度 I(0) i0	561256000.00
分子量 molecular_weight	187870.0 kDa
排除体积 excluded_volume	233150 Å³
包络体积 envelope_volume	269760 Å³
水化壳体积 shell_volume	64059 Å³
包络直径 envelope_diameter	99.2 Å
壳层 Rg shell_rg	42.79 Å
包络 Rg envelope_rg	32.38 Å
形状 Rg shape_rg	32.35 Å
总 Rg total_rg	33.07 Å
总原子数 total_atoms	13260
残基数 n_residues	1708
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	99.4 Å
Rg (实空间) rg_real	33.16 Å
Rg 误差 (实空间) rg_real_error	0.32 Å
I(0) (实空间) i0_real	5.6130e+08
I(0) 误差 (实空间) i0_real_error	7.0050e+06
Rg (倒空间) rg_reciprocal	33.30 Å
I(0) (倒空间) i0_reciprocal	561300000.0000
解质量估计 total_estimate	0.9030
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	44.4 Å
偏度 Skewness skewness	0.041
峰度 Kurtosis kurtosis	-0.578
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	352600000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.959

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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	ISOCITRATE LYASE
分子量 formula_weight	47205.5 kDa
EC 编号 ec_number	4.1.3.1
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	14276

MASVVGTPKSAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNALQRADQIAKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQNQMSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVDPNSSTTALTGSTEEGQFH

来源 Source

来源生物 organism	Mycobacterium tuberculosis H37Rv
NCBI 分类编号 ncbi_taxonomy_id	83332
宿主生物 host_organism	Escherichia coli

Entity 2 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	4

Entity 3 non-polymer

描述 description	PYRUVIC ACID
分子量 formula_weight	88.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	1016

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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	d1f8ma_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
家族 Family family	c.1.12.7 — Phosphoenolpyruvate mutase/Isocitrate lyase-like

结构域编号 domain_id	d1f8mb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
家族 Family family	c.1.12.7 — Phosphoenolpyruvate mutase/Isocitrate lyase-like

结构域编号 domain_id	d1f8mc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
家族 Family family	c.1.12.7 — Phosphoenolpyruvate mutase/Isocitrate lyase-like

结构域编号 domain_id	d1f8md_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
家族 Family family	c.1.12.7 — Phosphoenolpyruvate mutase/Isocitrate lyase-like

CATH v4.4 (4 domains)

结构域编号 domain_id	1f8mA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

结构域编号 domain_id	1f8mB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

结构域编号 domain_id	1f8mC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

结构域编号 domain_id	1f8mD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

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7. 引用文献 (1)

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晶胞边长 a length_a	74.310 Å
晶胞边长 b length_b	129.037 Å
晶胞边长 c length_c	166.165 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	1.800 Å
最低分辨率 resolution_low	19.860 Å
R 因子 r_factor	0.2030
R_work r_work	0.2030
R_free r_free	0.2470

fit	/app/data/saxs_computation/f8/1f8m/1f8m.fit
pddf	/app/data/pr_computation/f8/1f8m/1f8m.pr.out
profile	/app/data/saxs_computation/f8/1f8m/1f8m.dat

CRYSTAL STRUCTURE OF 3-BROMOPYRUVATE MODIFIED ISOCITRATE LYASE (ICL) FROM MYCOBACTERIUM TUBERCULOSIS

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