9h4v

Crystal structure of the adduct formed upon reaction of aurothiomalate with human serum transferrin (apo-form)

Method: X-RAY DIFFRACTION D_max: 156.9 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	9h4v
沉积日期 deposition_date	2024-10-21
结构标题 title	Crystal structure of the adduct formed upon reaction of aurothiomalate with human serum transferrin (apo-form)
关键词 keywords	Myochrysine, metallodrug, gold-based drugs, protein metalation, human transferrin, aurothiomalate, METAL TRANSPORT; METAL TRANSPORT
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	44.16 Å
回转半径 Rg (电子) rg_electron	44.47 Å
零角强度 I(0) i0	415302000.00
分子量 molecular_weight	155220.0 kDa
排除体积 excluded_volume	188180 Å³
包络体积 envelope_volume	261120 Å³
水化壳体积 shell_volume	52294 Å³
包络直径 envelope_diameter	167.2 Å
壳层 Rg shell_rg	45.03 Å
包络 Rg envelope_rg	44.16 Å
形状 Rg shape_rg	44.52 Å
总 Rg total_rg	44.33 Å
总原子数 total_atoms	10625
残基数 n_residues	1352
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	156.9 Å
Rg (实空间) rg_real	44.61 Å
Rg 误差 (实空间) rg_real_error	1.57 Å
I(0) (实空间) i0_real	4.1530e+08
I(0) 误差 (实空间) i0_real_error	8.4440e+06
Rg (倒空间) rg_reciprocal	44.17 Å
I(0) (倒空间) i0_reciprocal	415100000.0000
解质量估计 total_estimate	0.5889
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	43.6 Å
偏度 Skewness skewness	0.587
峰度 Kurtosis kurtosis	-0.095
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	25830000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.739; Stabil: 1.000; Sysdev: 0.005; Positv: 1.000; Valcen: 0.789; Smooth: 0.631

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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	Serotransferrin
分子量 formula_weight	75284.5 kDa
来源方法 src_method	nat
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	10649

VPDKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVVKKDSGFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVANFFSGSCAPCADGTDFPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDVAFVKHSTIFENLANKADRDQYELLCLDNTRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTCPEAPTDECKPVKWCALSHHERLKCDEWSVNSVGKIECVSAETTEDCIAKIMNGEADAMSLDGGFVYIAGKCGLVPVLAENYNKSDNCEDTPEAGYFAVAVVKKSASDLTWDNLKGKKSCHTAVGRTAGWNIPMGLLYNKINHCRFDEFFSEGCAPGSKKDSSLCKLCMGSGLNLCEPNNKEGYYGYTGAFRCLVEKGDVAFVKHQTVPQNTGGKNPDPWAKNLNEKDYELLCLDGTRKPVEEYANCHLARAPNHAVVTRKDKEACVHKILRQQQHLFGSNVTDCSGNFCLFRSETKDLLFRDDTVCLAKLHDRNTYEKYLGEEYVKAVGNLRKCSTSSLLEACTFRRP

Entity 2 non-polymer

描述 description	CITRIC ACID
分子量 formula_weight	192.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 3 non-polymer

描述 description	GOLD ION
分子量 formula_weight	197.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	19

Entity 4 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 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	8

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7. 引用文献 (1)

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晶胞边长 a length_a	84.472 Å
晶胞边长 b length_b	99.714 Å
晶胞边长 c length_c	198.388 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	8

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

分辨率 resolution	3.020 Å
最低分辨率 resolution_low	89.250 Å
R 因子 r_factor	0.2458
R_work r_work	0.2432
R_free r_free	0.2965

fit	/app/data/saxs_computation/h4/9h4v/9h4v.fit
pddf	/app/data/pr_computation/h4/9h4v/9h4v.pr.out
profile	/app/data/saxs_computation/h4/9h4v/9h4v.dat

Crystal structure of the adduct formed upon reaction of aurothiomalate with human serum transferrin (apo-form)

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