SAXSdb — 8p5s

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8p5s
沉积日期 deposition_date	2023-05-24
结构标题 title	Crystal structure of the homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum
关键词 keywords	2-oxoglutarate dehydrogenase; ODH, OXIDOREDUCTASE; OXIDOREDUCTASE
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	40.87 Å
回转半径 Rg (电子) rg_electron	41.33 Å
零角强度 I(0) i0	230635000.00
分子量 molecular_weight	120470.0 kDa
排除体积 excluded_volume	149420 Å³
包络体积 envelope_volume	203870 Å³
水化壳体积 shell_volume	44854 Å³
包络直径 envelope_diameter	166.4 Å
壳层 Rg shell_rg	41.92 Å
包络 Rg envelope_rg	42.31 Å
形状 Rg shape_rg	41.31 Å
总 Rg total_rg	41.44 Å
总原子数 total_atoms	8475
残基数 n_residues	1087
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	154.2 Å
Rg (实空间) rg_real	41.36 Å
Rg 误差 (实空间) rg_real_error	1.83 Å
I(0) (实空间) i0_real	2.3060e+08
I(0) 误差 (实空间) i0_real_error	4.5990e+06
Rg (倒空间) rg_reciprocal	40.88 Å
I(0) (倒空间) i0_reciprocal	230500000.0000
解质量估计 total_estimate	0.7475
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	35.6 Å
偏度 Skewness skewness	0.666
峰度 Kurtosis kurtosis	-0.103
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	62030000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.482; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.340; Smooth: 0.929

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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	2-oxoglutarate dehydrogenase E1/E2 component
分子量 formula_weight	124510.6 kDa
EC 编号 ec_number	1.2.4.2,2.3.1.61
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	8872

GKLPEPGQTPIRGIFKSIAKNMDISLEIPTATSVRDMPARLMFENRAMVNDQLKRTRGGKISFTHIIGYAMVKAVMAHPDMNNSYDVIDGKPTLIVPEHINLGLAIDLPQKDGSRALVVAAIKETEKMNFSEFLAAYEDIVARSRKGKLTMDDYQGVTVSLTNPGGIGTRHSVPRLTKGQGTIIGVGSMDYPAEFQGASEDRLAELGVGKLVTITSTYDHRVIQGAVSGEFLRTMSRLLTDDSFWDEIFDAMNVPYTPMRWAQDVPNTGVDKNTRVMQLIEAYRSRGHLIADTNPLSWVQPGMPVPDHRDLDIETHNLTIWDLDRTFNVGGFGGKETMTLREVLSRLRAAYTLKVGSEYTHILDRDERTWLQDRLEAGMPKPTQAEQKYILQKLNAAEAFENFLQTKYVGQKRFSLEGAEALIPLMDSAIDTAAGQGLDEVVIGMPHRGRLNVLFNIVGKPLASIFNEFEGQMEQGQIGGSGDVKYHLGSEGQHLQMFGDGEIKVSLTANPSHLEAVNPVMEGIVRAKQDYLDKGVDGKTVVPLLLHGDAAFAGLGIVPETINLAKLRGYDVGGTIHIVVNNQIGFTTTPDSSRSMHYATDYAKAFGCPVFHVNGDDPEAVVWVGQLATEYRRRFGKDVFIDLVCYRLRGHNEADDPSMTQPKMYELITGRETVRAQYTEDLLGRGDLSNEDAEAVVRDFHDQMESVFNEVKEGGKKQAEAQTGITGSQKLPHGLETNISREELLELGQAFANTPEGFNYHPRVAPVAKKRVSSVTEGGIDWAWGELLAFGSLANSGRLVRLAGEDSRRGTFTQRHAVAIDPATAEEFNPLHELAQSKGNNGKFLVYNSALTEYAGMGFEYGYSVGNEDSIVAWEAQFGDFANGAQTIIDEYVSSGEAKWGQTSKLILLLPHGYEGQGPDHSSARIERFLQLCAEGSMTVAQPSTPANHFHLLRRHALSDLKRPLVIFTPKSMLRNKAAASAPEDFTEVTKFQSVINDPNVADAAKVKKVMLVSGKLYYELAKRKEKDGRDDIAIVRIEMLHPIPFNRISEALAGYPNAEEVLFVQDEPANQGPWPFYQEHLPELIPNMPKMRRVSRRAQSSTATGVAKVHQLEEKQLIDEAFEA

来源 Source

来源生物 organism	Corynebacterium glutamicum ATCC 13032
NCBI 分类编号 ncbi_taxonomy_id	196627
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
分子量 formula_weight	238.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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 4 non-polymer

描述 description	ACETYL COENZYME *A
分子量 formula_weight	809.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	THIAMINE DIPHOSPHATE
分子量 formula_weight	425.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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 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	397

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6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	8p5sA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	559 — Chloramphenicol Acetyltransferase
同源超家族 H-superfamily homologous superfamily	10 — Chloramphenicol acetyltransferase-like domain

结构域编号 domain_id	8p5sA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

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7. 引用文献 (2)

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晶胞边长 a length_a	150.987 Å
晶胞边长 b length_b	150.987 Å
晶胞边长 c length_c	314.335 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	120.00 °
晶胞分子数 Z z_pdb	18

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	2.459 Å
最低分辨率 resolution_low	27.530 Å
R 因子 r_factor	0.2061
R_work r_work	0.2038
R_free r_free	0.2509

fit	/app/data/saxs_computation/p5/8p5s/8p5s.fit
pddf	/app/data/pr_computation/p5/8p5s/8p5s.pr.out
profile	/app/data/saxs_computation/p5/8p5s/8p5s.dat

Crystal structure of the homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution