8k9t

Cryo-EM structure of the products-bound PGAP1(Bst1)-S327A from Chaetonium thermophilum

Method: ELECTRON MICROSCOPY D_max: 118.1 Å Quality: REASONABLE

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	8k9t
沉积日期 deposition_date	2023-08-01
结构标题 title	Cryo-EM structure of the products-bound PGAP1(Bst1)-S327A from Chaetonium thermophilum
关键词 keywords	;Bst1, Glycosylphosphatidylinositol, GPI anchoring, GPI-AP, GPI-AP remodelase, Integral membrane enzyme, Lipase, Lipid remodeling, Membrane enzyme, Membrane protein, Nanodisc, PGAP1, TGP, Thermostable green fluorescence protein, Transmembrane enzyme, Triad enzyme. ;; MEMBRANE PROTEIN
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	33.53 Å
回转半径 Rg (电子) rg_electron	33.17 Å
零角强度 I(0) i0	338711000.00
分子量 molecular_weight	101850.0 kDa
排除体积 excluded_volume	99993 Å³
包络体积 envelope_volume	171630 Å³
水化壳体积 shell_volume	43778 Å³
包络直径 envelope_diameter	127.7 Å
壳层 Rg shell_rg	39.22 Å
包络 Rg envelope_rg	33.72 Å
形状 Rg shape_rg	33.16 Å
总 Rg total_rg	33.53 Å
总原子数 total_atoms	7747
残基数 n_residues	965
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	118.1 Å
Rg (实空间) rg_real	33.65 Å
Rg 误差 (实空间) rg_real_error	0.99 Å
I(0) (实空间) i0_real	3.3870e+08
I(0) 误差 (实空间) i0_real_error	5.4210e+06
Rg (倒空间) rg_reciprocal	33.57 Å
I(0) (倒空间) i0_reciprocal	338700000.0000
解质量估计 total_estimate	0.6683
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	35.2 Å
偏度 Skewness skewness	0.509
峰度 Kurtosis kurtosis	-0.078
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	53750000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.754; Stabil: 1.000; Sysdev: 0.214; Positv: 1.000; Valcen: 0.867; Smooth: 0.911

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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 (9)

Entity 1 polymer

描述 description	GPI inositol-deacylase,MCherry protein
分子量 formula_weight	161345.5 kDa
EC 编号 ec_number	3.1.-.-
突变 mutation	S327A,W148S,I166V,Q168Y,I202R
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	7747

MGSRSLSSASSDDDDAPPIRVPRVNQCATSRTKDSQSPAQSASKLDRRRSADRRPSFSANRRSGTGAGTGTGTGIANWRPFDSRDATVERAGSSTATTATTPPPSSSLGLMLAANGAVQEKEMVMMGKAQEHGFVGRRAPWRSPWAISVFAFVTSLLGIGLLLAVIHSSVTRQIDPKGCRMSYMRPSYAKLSDFDTEHTRLASKYSLYLYREQGIDHDVKVRGVPVLFIPGNAGSYKQVRPIAAEAANYFHDVLQHDEAALRAGVRSLDFFTVDFNEDITAFHGQTLLDQAEYLNEAIRYILSLYLDPRVSERDPDLPDPTSVIVLGHAMGGIVARTMLIMPNYQHNSINTIITMSAPHARPPVSFDGQIVQTYKDINNYWRHAYSQKWANDNPLWHVTLVSIAGGGLDTVVPSDYASIESLVPDTHGFTVFTSTIPNVWTSMDHQAILWCDQFRKVIIRALFDIVDVHRASQTKPRAQRMRVFKKWFLSGMETVAEKIAPTSDPTTLLIVDDKSDSITAEGERLVLRELGTQGSVRAHLMPIPPPGSPELKRFTLLTDTKLDKPGENGKLEVMFCSVIPSQPNPTGPAIPSQLDLSKGNAGTTRLACTNVAPDVITLPASTRFARFPFSVRKEAEIPPFSYLEYVLDDISEHQFVAVIEKATIPTPGFVIAEFSDHSNSHHTRHIGLRNLLTFGISLRLPSNRPMMSEVRIPSVKSSLLAYNLRISALECSGRKDLFAPLVRQYLAEPYESKYFVNARQAAVSLHGVAPYVPPPMSREPEAEGLAFQLWTDPTCNSSIQVDLTVDVMGSLGKLYMRYRTVFAAFPLFIVSLVLRKQFQVYDSTGSFITFAEGLDLSLRQSIPVMLIVLAALTLSTTKMAPSSSAGLWHWGGNTTFTNFHQNDLLIGTQDPFFLFLIPLIGIICVGVCTVVNYIALSLTRLISVVISFIGFLTVRFGWVNAEDRRRPSNPAIFPPSSPRRRMITTAVLLFLVSTMIPYQLAYLVACLVQLGTLVRAQRISSELRSPANSNFHNYVHSIFILMLWILPINLPTLVVWMHNLSVHWLTPFTSHHNVFSIMPFILLVETHTTGQMIPRTGGTGNGRCCVLLRHITSILLLSLALYAAVYGVSYAYTLHQFVNLFAFWLVMVHSTADDWSLTGLRQLILHNRNNANNKSETGSRKRGKEPGTLEVLFQGPKLEFVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGSEASSERMYPEDGALKGEVKYRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNRKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYKSAHHHHHHHHHH

来源 Source

来源生物 organism	Psychromonas sp. B3M02
NCBI 分类编号 ncbi_taxonomy_id	2267226
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	Green fluorescent protein,Complement decay-accelerating factor
分子量 formula_weight	29894.2 kDa
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	B

GGSGGSASVIKPEMKIKLRMEGAVNGHKFVIEGEGIGKPYEGTQTLDLTVEEGAPLPFSYDILTPAFQYGNRAFTKYPEDIPDYFKQAFPEGYSWERSMTYEDQGICIATSDITMEGDCFFYEIRFDGTNFPPNGPVMQKKTLKWEPSTEKMYVEDGVLKGDVEMALLLEGGGHYRCDFKTTYKAKKDVRLPDAHEVDHRIEILSHDKDYNKVRLYEHAEARYSGGGSGGGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKGSPNKGSGTTS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 non-polymer

描述 description	PALMITIC ACID
分子量 formula_weight	256.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	alpha-D-mannopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate
分子量 formula_weight	303.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	2-amino-2-deoxy-alpha-D-glucopyranose
分子量 formula_weight	179.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	;[(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z},11~{Z},14~{Z})-icosa-5,8,11,14-tetraenoate ;
分子量 formula_weight	873.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 non-polymer

描述 description	CHOLESTEROL
分子量 formula_weight	386.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 9 non-polymer

描述 description	2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate
分子量 formula_weight	303.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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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	—

分辨率 resolution	2.66 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	353585

fit	/app/data/saxs_computation/k9/8k9t/8k9t.fit
pddf	/app/data/pr_computation/k9/8k9t/8k9t.pr.out
profile	/app/data/saxs_computation/k9/8k9t/8k9t.dat

Cryo-EM structure of the products-bound PGAP1(Bst1)-S327A from Chaetonium thermophilum

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

5. 实体与聚合体信息 (9)

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

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)