SAXSdb — 8trz

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8trz
沉积日期 deposition_date	2023-08-10
结构标题 title	Cryo-EM structure of N-glycosylated Pomacea canaliculata hemocyanin
关键词 keywords	Glycoprotein, Respiratory Pigment, Cooper Protein, Carbohydrates, OXYGEN TRANSPORT; OXYGEN TRANSPORT
实验方法 method	ELECTRON MICROSCOPY

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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	— Å
回转半径 Rg (电子) rg_electron	166.70 Å
零角强度 I(0) i0	826544000000.00
分子量 molecular_weight	7775300.0 kDa
排除体积 excluded_volume	9694500 Å³
包络体积 envelope_volume	23693000 Å³
水化壳体积 shell_volume	1174400 Å³
包络直径 envelope_diameter	458.6 Å
壳层 Rg shell_rg	182.40 Å
包络 Rg envelope_rg	146.40 Å
形状 Rg shape_rg	166.70 Å
总 Rg total_rg	166.80 Å
总原子数 total_atoms	549912
残基数 n_residues	67750
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	470.6 Å
Rg (实空间) rg_real	166.60 Å
Rg 误差 (实空间) rg_real_error	1.29 Å
I(0) (实空间) i0_real	8.0080e+11
I(0) 误差 (实空间) i0_real_error	1.7590e+10
Rg (倒空间) rg_reciprocal	202.40 Å
I(0) (倒空间) i0_reciprocal	988200000000.0000
解质量估计 total_estimate	0.8718
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	261.5 Å
偏度 Skewness skewness	-0.239
峰度 Kurtosis kurtosis	-0.541
角度范围 angular_range	— – 0.0450 Å⁻¹
当前正则化参数 α current_alpha	2.0060
最高正则化参数 α highest_alpha	59640000000.0000
实空间数据点数 n_real_points	10
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.001; Oscil: 0.876; Stabil: 0.932; Sysdev: 1.000; Positv: 1.000; Valcen: 0.918; 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 (4)

Entity 1 polymer

描述 description	Hemocyanin
分子量 formula_weight	388727.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	20

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
原子数 atom_count	549912

SLVRKNVDLLTDQEVLSLESYLRELEDDKTVNGYQNLAAFHGEPSMCTKDDGKRVACCVHGMATFPQWHRLYVVQLEQKLGKKGLADIGVPYWDWTKPITALPRLVQEPIFKDPKGGLGQKNSWFSGEINVDSMDVHTSTARAVDDRLFQSVAPGENTQLFEMVLDALEEDDYCHFEVQFEVAHNHIHYLVGGRHDHSLSTLEWSAYDPLFFLHHSNVDRIFVIWQELQKKRGKTYDHADCSVELFRKKLEPFDRDTNPIELTRTYSTAKSLFSYRQLGYVYDDLSLNGLNIEQLYNLLEQRRARERALASFTLHGLGFSANVRIKVCDHDDDDDQSHSHCEFAGDIFILGGANEMPWEFNLPYHFDISKAVEHLGKKLNGDYVVTAELYSVNGTSLNPNLLPRPVGVYRPAKGFTDPKPSESDVQSANVVIRKDVDTLTDEEVYELRQALSRFQNDTSVNGYQSVAEFHGLPARCPRPDARVRYACCVHGMATFPHWHRLFVVQVEDALKSRGLHFGIPYWDWTRPGTTVPAIASKETYVDPNSGSSVHNPFFNAPVAFLGETTSRQVQPELSTKPEYGDHTALFDGMLLALEQRDFCDFEVQFEVVHNLPHFLVGGFASYSLSTLHYSAFDPIFILHHSNVDRLWAIWQALQIKRGLPYKAHCAHTMTHELLKPFGFAPPLNSNEKTYSHARPTNIYDYEHELEYAYDNLQFGGMTIDQLDHYIDERRTKDRTFVGLHLQNIGTSALVILSIKPKDGDSYEVAKLAVLGGEKEMPWNFDRLVKVEITDALNKKGLKYDDEYDVVLSIKDVSGKDWPENTFSHTTIIHEEGTTHEETGEHQELHVRSDVSSLTREQVQSLREALQSLEDDTSINGFEHIAAFHGQPNWCPSPDAEKKFACCAHGMAVFPHWHRLLTVQAENALRAKGFQDGLPYWDWTLPMTALPEIVAGETYVNPETNLPEPNPFHHGLVEGKKTTRSVRDELFEKPKFGRLTKIAEMVLLAFEQTDFCTFEVQYEIAHNYIHALVGGNESYSMASLRYTAYDPIFFLHHSNTDRIWAIWQALQHYRGLPYNSANCAIASLRKPLQPFAQTSTINPDHITRDHSVPFEVFDYERSFQYHYDDLEFNGFSIPQLQREILHRQHDERVFAGFMLHGIRKSALVTLEVCEPSGPCHPEGEFYILGDEYEIPWQYDRLFQYEITDILAKYKLEANDRYSVKYSVIDLDGKKISSEVFGKVTVVVRPGSETKKGEIDKNIVASSHIRRNLQDLSEGEVESLKSALRRMQDDGTFGKIASFHGFPSLCTHEGRKVACCVHGSAVFPHWHRLYVDQVENALLARGSAVSVPYWDWTQPIRQLPALINEASYFDSRSQTEESNPFFQVKILDTGKVTTRDPQPELFNSDYLLNNVLLALEQTSFCDFEIQFEIVHNALHSLVGGRGLYSLSSLDYSAFDPLFFLHHANVDRIWAIWQALQQYRGLPDDKSDCALNIMRQPLKPFNDKGQNEFDLTNRYSRPIDVFDYSNHFDYHYDTLNFNSWTIPQLEEVLKRQRAQDRLFAGFLLHNIGTSADVQLFICVATGNGERNCNHPAGSFSVLGGETEMPFIFDRLYKYDISDPVRKLGLKLDSAGDIDLEIKIRAYNGSYLESSVLRRPSLIFVPGEDNSQDQTGKTERRLIRKSVTSLTIGERRSLVLALQSLEEDSSATGFQALASFHAVPPLCPYPEANQRYACCVHGMATFPQWHRLYTVQFEDALRRRGALVGIPYWDTVNPQNSLPAFFNEPIYRDPVLDVDIPNPWAGADIAFENTTVERDFKRNRLSDDGEHGYDNWLWKQFLFALEQENYCDFEVQFEIAHNAIHAWVGGSKEHSMAHLHYASYDPIFLLHHSSTDRIYALWQELQRLRGHDPNEANCALELMREPLKPFSFGAPYNLDPITKEYSKPEDVFDYKSHFNYEYDTLELAGINAELLLSLINKQKEKSRAFAGFLLGGIKTSAHVDIKVCTPEDVCKDAGDFDVLGGTAEMPWSFDRLYRYEITEVLEKKGLSVDDAFTVKVELRALNGSILSSSLIPTPSVLYEPKSRVTSIQELPPNRVRHEISHLDARATMSLKAALRDLQKDGTKSGWQALAAFHGVPALCPSPEAPKYACCLHGVPTFPHWHRLYTLQVEQALLKHGSTVALPYWDWTLPISQLPSLFTEQTFYDAWKDEVLENPFARGYIKESKGYTVRDPQPELFKLSADGKHSVLFDEVLLVLEQTDYCDFEVQFEVTHNAIHYLVGGHQSYSLSSLHYSSYDPIFFTHHTFVDKIWAVWQELQKRRGLPYDRADCAVNYMSDAMQPFNSVVLNENAFTRTHALPKEVFNYQDLNFRYDDMKLGGLNLDELEEEIRQHQSKARVFAGFLLHGIGTSAEVRFSVCQENGKCTRAGAIFVLGGSLEMPWAFDRLYKYDITDTLNELHIRPEDVFNADAPFSLRYEIIAVNGTALPPSSLSKPTIIFKPAVGARTEEASYSVSGIGVRKNINTLTVAETESLKKALRAVQQQSGPRGYQEIAAAHGYPGLCKDNGHTVACCHHGSASFPQWHRLFVVTLERALTLQGARVGIPYWDWTESFTSLPTLLTDKDDNPFEHGEIASLNEKTTRSPRPQLFSDPERGEESFFYRQILLAFEQRDYCNFEVQYEVTHNAIHSWIGGTSPYGMSTLEYSAYDPIFFIHHSNVDRQFAIWQALQRYRGLDYNSANCNIQELRQPLEPFNWDSNPNDFIRENARAVDAFDYDQFNYQYDDLNFHGLTIPQLEEAIEKRRSEDRVFANFMLQGFKASADVTFDLCDADNHCSFAGTFAVLGGPLEMDWHFDRLFQYDVTSVFNQMHLRPDSVYHFDVHITAINGTQLASSLLESPSVSFVPGKGKTGSRAVAKEDPQPTKTKDVVRYEVSALSLEQVSNLRNALYKLQNDDGPNGYEAIASFHGAPKLCPENATDRYACCTHGMPVFPHWHRLLTVQFEMALRDKGALLGIPYWDWTRPSKALPSLLTSTDNNPFSTYQIKFAQHQVTRDVQPGLYNRRKQSGLDSLFYQTLETLEETNYCDFEVQFEMLHNTIHALVGGQGTYSMSTLEYSAFDPFFMIHHSSIDRIWQIWQTLQKLRHRSFNYARCALRNLYRPLEPFNYESKNPNPVTRANSRPVQIFDASKFHYNFDNLNLNGHSVSEINTIIENLRDHDRVYAGFVLSGIGVSATANVKLVPQGGDPVDVGSFYILGGDGEMPWAYERVYKYDVTDALEKLGLNAYSNFGFQVTLTKYNGEQLDASLATPVVISRPANADYDVLILPLLEENKLPPKVIVSRGTRVRFHSPVSSLNANVKEVGSYTSLSLCSIPPGDANSYDPDVNYSLEPGDYFFVSSNKARCEQGTRVQISIDDE

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	40

Entity 3 branched

描述 description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	60

Entity 4 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	20

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	triclinic

分辨率 resolution	4.40 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	29935

fit	/app/data/saxs_computation/tr/8trz/8trz.fit
pddf	/app/data/pr_computation/tr/8trz/8trz.pr.out
profile	/app/data/saxs_computation/tr/8trz/8trz.dat

Cryo-EM structure of N-glycosylated Pomacea canaliculata hemocyanin

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

冷冻电镜 EM 3D