8rjm

;Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its Pfr state (I0a). ;

Method: X-RAY DIFFRACTION D_max: 142.6 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	8rjm
沉积日期 deposition_date	2023-12-21
结构标题 title	;Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its Pfr state (I0a). ;
关键词 keywords	fluorescent protein, phytochrome, bacteriophytochrome, Pfr-state, optogenetic, SIGNALING PROTEIN; SIGNALING PROTEIN
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	41.03 Å
回转半径 Rg (电子) rg_electron	40.88 Å
零角强度 I(0) i0	180480000.00
分子量 molecular_weight	107750.0 kDa
排除体积 excluded_volume	134430 Å³
包络体积 envelope_volume	193280 Å³
水化壳体积 shell_volume	41912 Å³
包络直径 envelope_diameter	152.5 Å
壳层 Rg shell_rg	42.89 Å
包络 Rg envelope_rg	40.37 Å
形状 Rg shape_rg	40.93 Å
总 Rg total_rg	40.84 Å
总原子数 total_atoms	7579
残基数 n_residues	975
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	142.6 Å
Rg (实空间) rg_real	41.30 Å
Rg 误差 (实空间) rg_real_error	1.64 Å
I(0) (实空间) i0_real	1.8050e+08
I(0) 误差 (实空间) i0_real_error	3.5100e+06
Rg (倒空间) rg_reciprocal	41.03 Å
I(0) (倒空间) i0_reciprocal	180400000.0000
解质量估计 total_estimate	0.8336
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	52.5 Å
偏度 Skewness skewness	0.513
峰度 Kurtosis kurtosis	-0.094
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15330000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.887; Smooth: 0.605

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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 (6)

Entity 1 polymer

描述 description	histidine kinase
分子量 formula_weight	57507.5 kDa
EC 编号 ec_number	2.7.13.3
突变 mutation	;K69R, R83K, G120D, A123T, M163L, Q168E, R220P, S243N, V244F, G269D, A276V, Y270C, E294A, H303F, H333R, I336L, D349R, M351I, A386V, G409D, L419I, T469S, A487T, E494G ;
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	7974

MASTDYHVDLTNCDREPIHIPGYIQPHGCLIACDNAMRMVLRHSENCGELLGLEGDLNGRTAEDVLGKRLVHDLRNALTVTGKTTRPAMLPAMETSDGRSFDISLHRYKSTTIIEFEPSDSDTQPLGTARKMVDRIREADSVESLISRTTRLVKATLGYDRVLIYRFEEDGAGKVVSEAKQPELESFLGQYFPASDIPQQARALYLKNTLRIISDASGTPIPVLPAVDVSGEPLDLSYAHLRNFSPIHCEYLRNMGVAASMSISVIVDDALWGLIVCHHCSPRVLSMPVRIAAAMFGEFFSMFLQVLKQKRRLDTINHAHAALDRFLRLAAHRANLEELLVDSFQDFARLIPCDGVGLWVGNNWHGHGATPPHDAIPRLARFVASVSEGRVWATHALSQAIPEAEIYADTAAGMLAIPISQVKSDYLLFFRKEIVQNLNWAGNPEKSYETGPMGDRLTPRKSFAIWKESVRLQAQPWSEADREIAETARIALVGVAFHHSELMAGLEYKHHHHHH

来源 Source

来源生物 organism	Agrobacterium fabrum str. C58
NCBI 分类编号 ncbi_taxonomy_id	176299
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	;3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid ;
分子量 formula_weight	584.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 4 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 5 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	304

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7. 引用文献 (1)

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晶胞边长 a length_a	184.980 Å
晶胞边长 b length_b	184.980 Å
晶胞边长 c length_c	182.538 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	24

空间群 space_group	P 63 2 2
空间群编号 int_tables_number	182
晶系 crystal_system	—

分辨率 resolution	2.150 Å
最低分辨率 resolution_low	25.750 Å
R 因子 r_factor	0.2041
R_work r_work	0.2038
R_free r_free	0.2169

fit	/app/data/saxs_computation/rj/8rjm/8rjm.fit
pddf	/app/data/pr_computation/rj/8rjm/8rjm.pr.out
profile	/app/data/saxs_computation/rj/8rjm/8rjm.dat