9hnm

;Structure of the (6-4) photolyase of Caulobacter crescentus in its dark adapted and oxidized state determined by serial femtosecond crystallography ;

Method: X-RAY DIFFRACTION D_max: 85.8 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	9hnm
沉积日期 deposition_date	2024-12-11
结构标题 title	;Structure of the (6-4) photolyase of Caulobacter crescentus in its dark adapted and oxidized state determined by serial femtosecond crystallography ;
关键词 keywords	DNA repair, photolyase, electron transfer, iron-sulfur cluster, FLAVOPROTEIN; FLAVOPROTEIN
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	24.69 Å
回转半径 Rg (电子) rg_electron	23.61 Å
零角强度 I(0) i0	62782700.00
分子量 molecular_weight	59430.0 kDa
排除体积 excluded_volume	73280 Å³
包络体积 envelope_volume	85979 Å³
水化壳体积 shell_volume	29908 Å³
包络直径 envelope_diameter	87.8 Å
壳层 Rg shell_rg	31.30 Å
包络 Rg envelope_rg	23.91 Å
形状 Rg shape_rg	23.57 Å
总 Rg total_rg	24.53 Å
总原子数 total_atoms	4162
残基数 n_residues	508
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	85.8 Å
Rg (实空间) rg_real	24.62 Å
Rg 误差 (实空间) rg_real_error	0.76 Å
I(0) (实空间) i0_real	6.2780e+07
I(0) 误差 (实空间) i0_real_error	9.4820e+05
Rg (倒空间) rg_reciprocal	24.63 Å
I(0) (倒空间) i0_reciprocal	62780000.0000
解质量估计 total_estimate	0.7740
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	28.6 Å
偏度 Skewness skewness	0.317
峰度 Kurtosis kurtosis	-0.242
角度范围 angular_range	— – 0.3200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16900000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.704; Stabil: 0.989; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; 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 (5)

Entity 1 polymer

描述 description	Cryptochrome/photolyase family protein
分子量 formula_weight	58121.3 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	A
原子数 atom_count	4527

MAGALRLVLGDQLSDNLSALVDADLSRDQVLMVESRVEATAWKHHKQKLVLVWSAMRQFAERLRARGFNVRYVTLEDPDNTGSIGGELRRALEARAFDRVIRTACGKWGLESHLLSLDLPVPMETREDDRFLCSRAQFAAWAEGRRELRMEFFYREMRRKTGLLMDGDQPAGGRWNFDAENRRKLPPGLRPPERLRIPPNPTTQTVLEQVSRGFDDHFGEVEGFGWPTNPDEATAILDHFIADMLPSFGDWQDAMSWRRPFLWHSLISPALNIGLLDPLDICRRAEAAWREGRAPLNAVEGFIRQIIGWREFVRGIYWLKMPEYAQRNALDAQGKLPGFYWTGQTDMACVADTVRAAHDHAYAHHIQRLMVTGNLAMLLGVHPDAVDDWYMVVFADAYEWVEMPNTRGMATFADGGIVGSKPYAASGAYIDRMSDYCKGCRYDVKKRLGDDACPFNALYWDFIDRHAQRLAGNGRMMMPLRTLEKMPDAEREAFRKQARALRVKMGVSG

来源 Source

来源生物 organism	Caulobacter vibrioides
NCBI 分类编号 ncbi_taxonomy_id	155892
宿主生物 host_organism	Escherichia coli B

Entity 2 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol
分子量 formula_weight	326.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	274

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7. 引用文献 (1)

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晶胞边长 a length_a	49.800 Å
晶胞边长 b length_b	103.400 Å
晶胞边长 c length_c	104.800 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	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	orthorhombic

分辨率 resolution	1.710 Å
最低分辨率 resolution_low	24.230 Å
R 因子 r_factor	0.1600
R_work r_work	0.1586
R_free r_free	0.1874

fit	/app/data/saxs_computation/hn/9hnm/9hnm.fit
pddf	/app/data/pr_computation/hn/9hnm/9hnm.pr.out
profile	/app/data/saxs_computation/hn/9hnm/9hnm.dat

;Structure of the (6-4) photolyase of Caulobacter crescentus in its dark adapted and oxidized state determined by serial femtosecond crystallography ;

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