8rjn

;Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its Pfr state (I0b). ;

Method: X-RAY DIFFRACTION D_max: 142.9 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	8rjn
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 (I0b). ;
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	40.77 Å
回转半径 Rg (电子) rg_electron	40.68 Å
零角强度 I(0) i0	178674000.00
分子量 molecular_weight	107660.0 kDa
排除体积 excluded_volume	134480 Å³
包络体积 envelope_volume	192040 Å³
水化壳体积 shell_volume	41730 Å³
包络直径 envelope_diameter	151.2 Å
壳层 Rg shell_rg	42.96 Å
包络 Rg envelope_rg	40.20 Å
形状 Rg shape_rg	40.74 Å
总 Rg total_rg	40.62 Å
总原子数 total_atoms	7582
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	142.9 Å
Rg (实空间) rg_real	41.04 Å
Rg 误差 (实空间) rg_real_error	1.75 Å
I(0) (实空间) i0_real	1.7870e+08
I(0) 误差 (实空间) i0_real_error	3.5920e+06
Rg (倒空间) rg_reciprocal	40.77 Å
I(0) (倒空间) i0_reciprocal	178600000.0000
解质量估计 total_estimate	0.6157
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	51.3 Å
偏度 Skewness skewness	0.510
峰度 Kurtosis kurtosis	-0.081
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16840000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 0.107; Positv: 1.000; Valcen: 0.749; Smooth: 0.630

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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	histidine kinase
分子量 formula_weight	56678.6 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	7828

MASTDYHVDLTNCDREPIHIPGYIQPHGCLIACDNAMRMVLRHSENCGELLGLEGDLNGRTAEDVLGKRLVHDLRNALTVTGKTTRPAMLPAMETSDGRSFDISLHRYKSTTIIEFEPSDSDTQPLGTARKMVDRIREADSVESLISRTTRLVKATLGYDRVLIYRFEEDGAGKVVSEAKQPELESFLGQYFPASDIPQQARALYLKNTLRIISDASGTPIPVLPAVDVSGEPLDLSYAHLRNFSPIHCEYLRNMGVAASMSISVIVDDALWGLIVCHHCSPRVLSMPVRIAAAMFGEFFSMFLQVLKQKRRLDTINHAHAALDRFLRLAAHRANLEELLVDSFQDFARLIPCDGVGLWVGNNWHGHGATPPHDAIPRLARFVASVSEGRVWATHALSQAIPEAEIYADTAAGMLAIPISQVKSDYLLFFRKEIVQNLNWAGNPEKSYETGPMGDRLTPRKSFAIWKESVRLQAQPWSEADREIAETARIALVGVAFHHSELMAGLEYK

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 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	216

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7. 引用文献 (1)

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晶胞边长 a length_a	184.192 Å
晶胞边长 b length_b	184.192 Å
晶胞边长 c length_c	181.633 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	2.200 Å
最低分辨率 resolution_low	92.270 Å
R 因子 r_factor	0.2138
R_work r_work	0.2132
R_free r_free	0.2414

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

;Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its Pfr state (I0b). ;

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