SAXSdb — 1hsr

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hsr
沉积日期 deposition_date	1997-07-01
结构标题 title	BINDING MODE OF BENZHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE
关键词 keywords	OXIDOREDUCTASE, GLYCOPROTEIN, PEROXIDASE; OXIDOREDUCTASE
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	20.56 Å
回转半径 Rg (电子) rg_electron	19.48 Å
零角强度 I(0) i0	23789900.00
分子量 molecular_weight	36360.0 kDa
排除体积 excluded_volume	45025 Å³
包络体积 envelope_volume	50525 Å³
水化壳体积 shell_volume	21533 Å³
包络直径 envelope_diameter	65.6 Å
壳层 Rg shell_rg	26.15 Å
包络 Rg envelope_rg	19.77 Å
形状 Rg shape_rg	19.48 Å
总 Rg total_rg	20.32 Å
总原子数 total_atoms	2548
残基数 n_residues	336
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	65.5 Å
Rg (实空间) rg_real	20.47 Å
Rg 误差 (实空间) rg_real_error	0.25 Å
I(0) (实空间) i0_real	2.3790e+07
I(0) 误差 (实空间) i0_real_error	2.7870e+05
Rg (倒空间) rg_reciprocal	20.49 Å
I(0) (倒空间) i0_reciprocal	23790000.0000
解质量估计 total_estimate	0.8950
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	25.6 Å
偏度 Skewness skewness	0.247
峰度 Kurtosis kurtosis	-0.358
角度范围 angular_range	— – 0.3850 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	6181000.0000
实空间数据点数 n_real_points	70
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 1.000

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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 (6)

Entity 1 polymer

描述 description	PEROXIDASE
分子量 formula_weight	35722.8 kDa
EC 编号 ec_number	1.11.1.7
来源方法 src_method	nat
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	2789

QGPGGGGGSVTCPGGQSTSNSQCCVWFDVLDDLQTNFYQGSKCESPVRKILRIVFHDAIGFSPALTAAGQFGGGGADGSIIAHSNIELAFPANGGLTDTIEALRAVGINHGVSFGDLIQFATAVGMSNCPGSPRLEFLTGRSNSSQPSPPSLIPGPGNTVTAILDRMGDAGFSPDEVVDLLAAHSLASQEGLNSAIFRSPLDSTPQVFDTQFYIETLLKGTTQPGPSLGFAEELSPFPGEFRMRSDALLARDSRTACRWQSMTSSNEVMGQRYRAAMAKMSVLGFDRNALTDCSDVIPSAVSNNAAPVIPGGLTVDDIEVSCPSEPFPEIATASGPLPSLAPAP

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	PROTOPORPHYRIN IX CONTAINING FE
分子量 formula_weight	616.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	BENZHYDROXAMIC ACID
分子量 formula_weight	137.1 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	241

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6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1hsra_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.93 — Heme-dependent peroxidases
超家族 Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
家族 Family family	a.93.1.1 — CCP-like

CATH v4.4 (2 domains)

结构域编号 domain_id	1hsrA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	520 — Peroxidase; domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1hsrA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	420 — Peroxidase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Peroxidase, domain 2

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7. 引用文献 (6)

;Binding mode of benzhydroxamic acid to Arthromyces ramosus peroxidase shown by X-ray crystallographic analysis of the complex at 1.6 A resolution. ;

FEBS Lett. (1997)

PMID: 9257700 · DOI: 10.1016/S0014-5793(97)00751-5 PRIMARY

;Binding of Iodide to Arthromyces Ramosus Peroxidase Investigated with X-Ray Crystallographic Analysis, 1H and 127I NMR Spectroscopy, and Steady-State Kinetics ;

J.Biol.Chem. (1997)

Pentacoordination of the Heme Iron of Arthromyces Ramosus Peroxidase Shown by a 1.8 A Resolution Crystallographic Study at Ph 4.5

FEBS Lett. (1996)

;Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different Ph Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis ;

J.Biol.Chem. (1995)

;Crystal Structure of the Fungal Peroxidase from Arthromyces Ramosus at 1.9 A Resolution. Structural Comparisons with the Lignin and Cytochrome C Peroxidases ;

J.Mol.Biol. (1994)

Crystallization and Preliminary X-Ray Diffraction Studies of Peroxidase from a Fungus Arthromyces Ramosus

Proteins (1993)

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晶胞边长 a length_a	74.500 Å
晶胞边长 b length_b	74.500 Å
晶胞边长 c length_c	118.010 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 42 21 2
空间群编号 int_tables_number	94
晶系 crystal_system	—

分辨率 resolution	1.600 Å
最低分辨率 resolution_low	7.000 Å
R 因子 r_factor	0.1870
R_work r_work	0.1870
R_free r_free	—

fit	/app/data/saxs_computation/hs/1hsr/1hsr.fit
pddf	/app/data/pr_computation/hs/1hsr/1hsr.pr.out
profile	/app/data/saxs_computation/hs/1hsr/1hsr.dat

BINDING MODE OF BENZHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution