8owl

SR Ca(2+)-ATPase in the E2 state complexed with the photoswitch-thapsigargin derivative AzTG-6

Method: X-RAY DIFFRACTION D_max: 127.8 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	8owl
沉积日期 deposition_date	2023-04-28
最后修订 last_revision	2023-06-21
结构标题 title	SR Ca(2+)-ATPase in the E2 state complexed with the photoswitch-thapsigargin derivative AzTG-6
关键词 keywords	SERCA inhibitors, Photoswitch, Azobenzene, Thapsigargin, HYDROLASE; HYDROLASE
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	37.94 Å
回转半径 Rg (电子) rg_electron	38.50 Å
零角强度 I(0) i0	173613000.00
分子量 molecular_weight	109030.0 kDa
排除体积 excluded_volume	137590 Å³
包络体积 envelope_volume	180900 Å³
水化壳体积 shell_volume	41855 Å³
包络直径 envelope_diameter	136.2 Å
壳层 Rg shell_rg	41.21 Å
包络 Rg envelope_rg	38.35 Å
形状 Rg shape_rg	38.55 Å
总 Rg total_rg	38.48 Å
总原子数 total_atoms	7642
残基数 n_residues	981
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	127.8 Å
Rg (实空间) rg_real	38.38 Å
Rg 误差 (实空间) rg_real_error	1.41 Å
I(0) (实空间) i0_real	1.7360e+08
I(0) 误差 (实空间) i0_real_error	2.9690e+06
Rg (倒空间) rg_reciprocal	38.11 Å
I(0) (倒空间) i0_reciprocal	173600000.0000
解质量估计 total_estimate	0.8238
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	36.5 Å
偏度 Skewness skewness	0.559
峰度 Kurtosis kurtosis	-0.308
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	26000000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.859; Smooth: 0.515

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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	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
分子量 formula_weight	109303.2 kDa
EC 编号 ec_number	7.2.2.10
来源方法 src_method	nat
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	7642

MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALKEYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMAATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAVALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQMSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMKKEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGMLDPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAMGSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAIGGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLKALDLTQWLMVLKISLPVIGLDEILKFIARNY

Entity 2 non-polymer

描述 description	ACETYL GROUP
分子量 formula_weight	44.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	;[(3S,3aR,4S,6S,6aR,7S,8S,9bS)-6-acetyloxy-3,6,9-trimethyl-8-[(Z)-2-methylbut-2-enoyl]oxy-3,3a-bis(oxidanyl)-2-oxidanylidene-4-[6-[4-[(E)-phenyldiazenyl]phenyl]hexanoyloxy]-4,5,6a,7,8,9b-hexahydroazuleno[4,5-b]furan-7-yl] octanoate ;
分子量 formula_weight	859.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

结构域编号 domain_id	8owlA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1110 — Calcium-transporting ATPase, cytoplasmic domain N
同源超家族 H-superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic domain N

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7. 引用文献 (1)

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晶胞边长 a length_a	71.140 Å
晶胞边长 b length_b	71.140 Å
晶胞边长 c length_c	587.670 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 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	tetragonal

分辨率 resolution	3.020 Å
最低分辨率 resolution_low	73.460 Å
R 因子 r_factor	0.2218
R_work r_work	0.2207
R_free r_free	0.2427

fit	/app/data/saxs_computation/ow/8owl/8owl.fit
pddf	/app/data/pr_computation/ow/8owl/8owl.pr.out
profile	/app/data/saxs_computation/ow/8owl/8owl.dat

SR Ca(2+)-ATPase in the E2 state complexed with the photoswitch-thapsigargin derivative AzTG-6

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