SAXSdb — 2c88

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2c88
沉积日期 deposition_date	2005-12-02
结构标题 title	Crystal Structure Of (SR) Calcium-ATPase E2(Tg):AMPPCP form
关键词 keywords	CATION PUMP, MEMBRANE PROTEIN, MODULATORY ATP, HYDROLASE, ION TRANSPORT; 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	38.10 Å
回转半径 Rg (电子) rg_electron	38.77 Å
零角强度 I(0) i0	181777000.00
分子量 molecular_weight	110670.0 kDa
排除体积 excluded_volume	139270 Å³
包络体积 envelope_volume	181560 Å³
水化壳体积 shell_volume	41815 Å³
包络直径 envelope_diameter	138.7 Å
壳层 Rg shell_rg	41.10 Å
包络 Rg envelope_rg	38.71 Å
形状 Rg shape_rg	38.83 Å
总 Rg total_rg	38.69 Å
总原子数 total_atoms	7750
残基数 n_residues	994
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	129.5 Å
Rg (实空间) rg_real	38.56 Å
Rg 误差 (实空间) rg_real_error	1.41 Å
I(0) (实空间) i0_real	1.8180e+08
I(0) 误差 (实空间) i0_real_error	3.0280e+06
Rg (倒空间) rg_reciprocal	38.28 Å
I(0) (倒空间) i0_reciprocal	181700000.0000
解质量估计 total_estimate	0.5863
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	34.7 Å
偏度 Skewness skewness	0.564
峰度 Kurtosis kurtosis	-0.312
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	27960000.0000
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: 0.749; Stabil: 0.999; Sysdev: 0.035; Positv: 1.000; Valcen: 0.796; Smooth: 0.470

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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	SARCOPLASMIC-ENDOPLASMIC RETICULUM CALCIUM ATPASE1 ISOFORM SERCA1A
分子量 formula_weight	109602.6 kDa
EC 编号 ec_number	3.6.3.8
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	7750

MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALKEYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMAATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAVALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQMSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMKKEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGMLDPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAMGSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAIGGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLKALDLTQWLMVLKISLPVIGLDEILKFIARNYLEG

Entity 2 non-polymer

描述 description	;OCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OX Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER ;
分子量 formula_weight	650.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
分子量 formula_weight	505.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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 5 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) 4 domains

CATH v4.4 (4 domains)

结构域编号 domain_id	2c88A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	150 — Calcium-transporting ATPase, cytoplasmic transduction domain A
同源超家族 H-superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic transduction domain A

结构域编号 domain_id	2c88A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1110 — Calcium-transporting ATPase, transmembrane domain
同源超家族 H-superfamily homologous superfamily	10 — Calcium-transporting ATPase, transmembrane domain

结构域编号 domain_id	2c88A03
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	1000 — HAD superfamily/HAD-like

结构域编号 domain_id	2c88A04
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	71.529 Å
晶胞边长 b length_b	71.529 Å
晶胞边长 c length_c	590.216 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	—

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	14.990 Å
R 因子 r_factor	0.2610
R_work r_work	0.2610
R_free r_free	0.3100

fit	/app/data/saxs_computation/c8/2c88/2c88.fit
pddf	/app/data/pr_computation/c8/2c88/2c88.pr.out
profile	/app/data/saxs_computation/c8/2c88/2c88.dat

Crystal Structure Of (SR) Calcium-ATPase E2(Tg):AMPPCP form

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