8p5r

Crystal structure of full-length, homohexameric 2-oxoglutarate dehydrogenase KGD from Mycobacterium smegmatis in complex with GarA

Method: X-RAY DIFFRACTION D_max: 240.1 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8p5r
沉积日期 deposition_date	2023-05-24
结构标题 title	Crystal structure of full-length, homohexameric 2-oxoglutarate dehydrogenase KGD from Mycobacterium smegmatis in complex with GarA
关键词 keywords	2-oxoglutarate dehydrogenase; ODH; KGD; OXIDOREDUCTASE, 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	71.35 Å
回转半径 Rg (电子) rg_electron	71.04 Å
零角强度 I(0) i0	9390010000.00
分子量 molecular_weight	808870.0 kDa
排除体积 excluded_volume	1006200 Å³
包络体积 envelope_volume	1452800 Å³
水化壳体积 shell_volume	165780 Å³
包络直径 envelope_diameter	226.5 Å
壳层 Rg shell_rg	75.92 Å
包络 Rg envelope_rg	68.58 Å
形状 Rg shape_rg	71.06 Å
总 Rg total_rg	71.06 Å
总原子数 total_atoms	57005
残基数 n_residues	7346
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	240.1 Å
Rg (实空间) rg_real	71.16 Å
Rg 误差 (实空间) rg_real_error	1.92 Å
I(0) (实空间) i0_real	9.3910e+09
I(0) 误差 (实空间) i0_real_error	2.0870e+08
Rg (倒空间) rg_reciprocal	71.94 Å
I(0) (倒空间) i0_reciprocal	9404000000.0000
解质量估计 total_estimate	0.8136
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	98.2 Å
偏度 Skewness skewness	0.086
峰度 Kurtosis kurtosis	-0.579
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.0061
最高正则化参数 α highest_alpha	361300000.0000
实空间数据点数 n_real_points	23
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.000

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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 (5)

Entity 1 polymer

描述 description	Multifunctional 2-oxoglutarate metabolism enzyme
分子量 formula_weight	138548.1 kDa
EC 编号 ec_number	2.2.1.5,4.1.1.71,1.2.4.2,2.3.1.61
来源方法 src_method	man
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,N,O,P,Q
原子数 atom_count	57005

MGSSHHHHHHSSGLVPRGSHMASVSSSPSPFGQNEWLVEEMYRKFRDDPSSVDPSWHEFLVDYSPEPTTDSASNGRTTTAAPVTPPTPAPAPAPEPKAAPKPAAKTEAKPAKPAKSATPAKGDESQILRGAAAAVVKNMNASLEVPTATSVRAIPAKLMIDNRVVINNHLKRTRGGKISFTHLLGYAIVQAVKKFPNMNRHFAVVDGKPTAITPAHTNLGLAIDLQGKDGNRSLVVAAIKRCETMRFGQFIAAYEDIVRRARDGKLTAEDFSGVTISLTNPGTLGTVHSVPRLMQGQGAIIGAGAMEYPAEFQGASEERIADLGIGKLITLTSTYDHRIIQGAESGDFLRTIHQLLLDDDFFDEIFRELGIPYEPVRWRTDNPDSIEDKNARVIELIAAYRNRGHLMADIDPLRLDNTRFRSHPDLDVNSHGLTLWDLDREFKVDGFAGVQRKKLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHGSGDVKYHLGATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQLERVFNEVRELEKHEIEPSESVEADQQIPSKLATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG

来源 Source

来源生物 organism	Mycolicibacterium smegmatis MC2 155
NCBI 分类编号 ncbi_taxonomy_id	246196
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Glycogen accumulation regulator GarA
分子量 formula_weight	16599.0 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G,H,I,J,K,L

MTDKDSNLGADQSEDVTVETTSVFRADFLNELDAPAAAGTEGAVSGVEGLPSGSALLVVKRGPNAGSRFLLDQPTTSAGRHPDSDIFLDDVTVSRRHAEFRLEGGEFQVVDVGSLNGTYVNREPVDSAVLANGDEVQIGKFRLVFLTGPKSDDSGSNA

来源 Source

来源生物 organism	Mycolicibacterium smegmatis MC2 155
NCBI 分类编号 ncbi_taxonomy_id	246196
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	6

Entity 4 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	6

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7. 引用文献 (2)

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晶胞边长 a length_a	325.750 Å
晶胞边长 b length_b	325.750 Å
晶胞边长 c length_c	396.944 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	60

空间群 space_group	P 65
空间群编号 int_tables_number	170
晶系 crystal_system	—

分辨率 resolution	4.562 Å
最低分辨率 resolution_low	45.990 Å
R 因子 r_factor	0.1998
R_work r_work	0.1983
R_free r_free	0.2292

fit	/app/data/saxs_computation/p5/8p5r/8p5r.fit
pddf	/app/data/pr_computation/p5/8p5r/8p5r.pr.out
profile	/app/data/saxs_computation/p5/8p5r/8p5r.dat

Crystal structure of full-length, homohexameric 2-oxoglutarate dehydrogenase KGD from Mycobacterium smegmatis in complex with GarA

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

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)