SAXSdb — 1n8w

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1n8w
沉积日期 deposition_date	2002-11-21
结构标题 title	Biochemical and Structural Studies of Malate Synthase from Mycobacterium tuberculosis
关键词 keywords	;MALATE SYNTHASE, GLYOXYLATE PATHWAY, MYCOBACTERIUM TUBERCULOSIS, MALATE, COENZYME A, GLCB, GLYOXYLATE, 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	38.43 Å
回转半径 Rg (电子) rg_electron	38.08 Å
零角强度 I(0) i0	388122000.00
分子量 molecular_weight	157280.0 kDa
排除体积 excluded_volume	195690 Å³
包络体积 envelope_volume	252150 Å³
水化壳体积 shell_volume	55266 Å³
包络直径 envelope_diameter	140.6 Å
壳层 Rg shell_rg	44.07 Å
包络 Rg envelope_rg	37.45 Å
形状 Rg shape_rg	38.08 Å
总 Rg total_rg	38.42 Å
总原子数 total_atoms	11057
残基数 n_residues	1433
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	133.9 Å
Rg (实空间) rg_real	38.50 Å
Rg 误差 (实空间) rg_real_error	1.38 Å
I(0) (实空间) i0_real	3.8810e+08
I(0) 误差 (实空间) i0_real_error	7.0530e+06
Rg (倒空间) rg_reciprocal	38.46 Å
I(0) (倒空间) i0_reciprocal	388100000.0000
解质量估计 total_estimate	0.8736
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	42.5 Å
偏度 Skewness skewness	0.378
峰度 Kurtosis kurtosis	-0.330
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	72610000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.933

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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	Probable malate synthase G
分子量 formula_weight	80488.8 kDa
EC 编号 ec_number	4.1.3.2
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	11696

MTDRVSVGNLRIARVLYDFVNNEALPGTDIDPDSFWAGVDKVVADLTPQNQALLNARDELQAQIDKWHRRRVIEPIDMDAYRQFLTEIGYLLPEPDDFTITTSGVDAEITTTAGPQLVVPVLNARFALNAANARWGSLYDALYGTDVIPETDGAEKGPTYNKVRGDKVIAYARKFLDDSVPLSSGSFGDATGFTVQDGQLVVALPDKSTGLANPGQFAGYTGAAESPTSVLLINHGLHIEILIDPESQVGTTDRAGVKDVILESAITTIMDFEDSVAAVDAADKVLGYRNWLGLNKGDLAAAVDKDGTAFLRVLNRDRNYTAPGGGQFTLPGRSLMFVRNVGHLMTNDAIVDTDGSEVFEGIMDALFTGLIAIHGLKASDVNGPLINSRTGSIYIVKPKMHGPAEVAFTCELFSRVEDVLGLPQNTMKIGIMDEERRTTVNLKACIKAAADRVVFINTGFLDRTGDEIHTSMEAGPMVRKGTMKSQPWILAYEDHNVDAGLAAGFSGRAQVGKGMWTMTELMADMVETKIAQPRAGASTAWVPSPTAATLHALHYHQVDVAAVQQGLAGKRRATIEQLLTIPLAKELAWAPDEIREEVDNNCQSILGYVVRWVDQGVGCSKVPDIHDVALMEDRATLRISSQLLANWLRHGVITSADVRASLERMAPLVDRQNAGDVAYRPMAPNFDDSIAFLAAQELILSGAQQPNGYTEPILHRRRREFKARAAEKPAPSDRAGDDAAR

来源 Source

来源生物 organism	Mycobacterium tuberculosis
NCBI 分类编号 ncbi_taxonomy_id	1773
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	2

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	3

Entity 4 non-polymer

描述 description	D-MALATE
分子量 formula_weight	134.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 5 non-polymer

描述 description	COENZYME A
分子量 formula_weight	767.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	GLYOXYLIC ACID
分子量 formula_weight	74.0 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	639

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1n8wa_
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.1.13 — Malate synthase G
家族 Family family	c.1.13.1 — Malate synthase G

结构域编号 domain_id	d1n8wb_
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.1.13 — Malate synthase G
家族 Family family	c.1.13.1 — Malate synthase G

CATH v4.4 (6 domains)

结构域编号 domain_id	1n8wA01
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	360 — Malate synthase, domain 3

结构域编号 domain_id	1n8wA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	170 — Malate synthase G - maily-beta sub-domain
同源超家族 H-superfamily homologous superfamily	11 — Malate synthase G - maily-beta sub-domain

结构域编号 domain_id	1n8wA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1220 — Malate Synthase G; Chain: A; Domain 4
同源超家族 H-superfamily homologous superfamily	12 — Malate synthase, domain III

结构域编号 domain_id	1n8wB01
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	360 — Malate synthase, domain 3

结构域编号 domain_id	1n8wB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	170 — Malate synthase G - maily-beta sub-domain
同源超家族 H-superfamily homologous superfamily	11 — Malate synthase G - maily-beta sub-domain

结构域编号 domain_id	1n8wB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1220 — Malate Synthase G; Chain: A; Domain 4
同源超家族 H-superfamily homologous superfamily	12 — Malate synthase, domain III

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7. 引用文献 (1)

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晶胞边长 a length_a	120.985 Å
晶胞边长 b length_b	120.985 Å
晶胞边长 c length_c	232.787 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 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	29.360 Å
R 因子 r_factor	0.2002
R_work r_work	0.1905
R_free r_free	0.2872

fit	/app/data/saxs_computation/n8/1n8w/1n8w.fit
pddf	/app/data/pr_computation/n8/1n8w/1n8w.pr.out
profile	/app/data/saxs_computation/n8/1n8w/1n8w.dat

Biochemical and Structural Studies of Malate Synthase from Mycobacterium tuberculosis

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution