9dz3

Photoactivation in Bacteriophytochromes, reference (dark) structure for the 3 ps time point

Method: X-RAY DIFFRACTION D_max: 107.6 Å Quality: EXCELLENT

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9dz3
沉积日期 deposition_date	2024-10-15
最后修订 last_revision	2025-10-08
结构标题 title	Photoactivation in Bacteriophytochromes, reference (dark) structure for the 3 ps time point
关键词 keywords	Red-light receptor enzyme Bacteriophytochrome Myxobacteria Photosensory Core Domain, SIGNALING PROTEIN; SIGNALING PROTEIN
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	35.02 Å
回转半径 Rg (电子) rg_electron	34.51 Å
零角强度 I(0) i0	168352000.00
分子量 molecular_weight	105090.0 kDa
排除体积 excluded_volume	132210 Å³
包络体积 envelope_volume	174870 Å³
水化壳体积 shell_volume	42451 Å³
包络直径 envelope_diameter	106.7 Å
壳层 Rg shell_rg	40.92 Å
包络 Rg envelope_rg	33.95 Å
形状 Rg shape_rg	34.52 Å
总 Rg total_rg	34.97 Å
总原子数 total_atoms	7417
残基数 n_residues	964
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	107.6 Å
Rg (实空间) rg_real	34.88 Å
Rg 误差 (实空间) rg_real_error	0.82 Å
I(0) (实空间) i0_real	1.6840e+08
I(0) 误差 (实空间) i0_real_error	2.8640e+06
Rg (倒空间) rg_reciprocal	34.97 Å
I(0) (倒空间) i0_reciprocal	168400000.0000
解质量估计 total_estimate	0.9104
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	0
主峰位置 r_peak_primary	— Å
偏度 Skewness skewness	0.076
峰度 Kurtosis kurtosis	-0.752
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	31440000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.940

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	Photoreceptor-histidine kinase BphP
分子量 formula_weight	51981.5 kDa
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	7488

DLSQCDREPIHLLGGIQSHGVLLAFRGPDRLLEVVSANAQALLGRPPETLLGQPVGRVLPAEVLAQWEPLVARGSVRVVLPAGAYRALLHESDGLTVLELEPAELQPGMEETALEVVRRLVSPLAGVKGTQALLQTAADTVRALTGFDRVMVYRFDADWHGEVLAESKRGGMDGFLGMHFPATDIPVQARALYTRNPLRLIADARARPVPLLPPVVPALGRPLDLSNSALRSVSPVHLEYLRNMGVGASFSLSLLKEGVLWGLIACHHLEPLHISHERRRACEVLTQLLALQLSAEERAAEASEDAHRAALLGQLATAMGEGGTLEEVLEKESERVLALTGAAGVALLLGEEPLLVGCTPAQDEVEALVAWLATQPFQTSFHTDRLGTVYPPLAARADVAAGILAVRLAPAAARFAIWFRPEVARTISWAGNPRKPAEPEPGHQRLHPRGSFQAWEETVRDTSLPWKRADLGAAEGFRGALV

来源 Source

来源生物 organism	Stigmatella aurantiaca
NCBI 分类编号 ncbi_taxonomy_id	41
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	;3-[2-[[5-[[(3E,4S)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid ;
分子量 formula_weight	588.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	BENZAMIDINE
分子量 formula_weight	120.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	61

▶

7. 引用文献 (2)

▶

晶胞边长 a length_a	83.580 Å
晶胞边长 b length_b	83.040 Å
晶胞边长 c length_c	86.790 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	107.74 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	monoclinic

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	27.300 Å
R 因子 r_factor	0.1939
R_work r_work	0.1908
R_free r_free	0.2509

fit	/app/data/saxs_computation/dz/9dz3/9dz3.fit
pddf	/app/data/pr_computation/dz/9dz3/9dz3.pr.out
profile	/app/data/saxs_computation/dz/9dz3/9dz3.dat

Photoactivation in Bacteriophytochromes, reference (dark) structure for the 3 ps time point

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