SAXSdb — 1qfx

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1qfx
沉积日期 deposition_date	1999-04-15
结构标题 title	PH 2.5 ACID PHOSPHATASE FROM ASPERGILLUS NIGER
关键词 keywords	PHOSPHOMONOESTERASE, HYDROLASE; HYDROLASE
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	31.09 Å
回转半径 Rg (电子) rg_electron	30.14 Å
零角强度 I(0) i0	175468000.00
分子量 molecular_weight	102290.0 kDa
排除体积 excluded_volume	126190 Å³
包络体积 envelope_volume	153610 Å³
水化壳体积 shell_volume	41460 Å³
包络直径 envelope_diameter	113.0 Å
壳层 Rg shell_rg	38.12 Å
包络 Rg envelope_rg	30.56 Å
形状 Rg shape_rg	30.09 Å
总 Rg total_rg	30.96 Å
总原子数 total_atoms	7187
残基数 n_residues	884
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	104.2 Å
Rg (实空间) rg_real	31.02 Å
Rg 误差 (实空间) rg_real_error	0.82 Å
I(0) (实空间) i0_real	1.7550e+08
I(0) 误差 (实空间) i0_real_error	2.8660e+06
Rg (倒空间) rg_reciprocal	31.05 Å
I(0) (倒空间) i0_reciprocal	175500000.0000
解质量估计 total_estimate	0.8873
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	34.7 Å
偏度 Skewness skewness	0.270
峰度 Kurtosis kurtosis	-0.425
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	41290000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.986

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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 (7)

Entity 1 polymer

描述 description	PROTEIN (PH 2.5 ACID PHOSPHATASE)
分子量 formula_weight	50879.9 kDa
EC 编号 ec_number	3.1.3.8
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	7835

FSYGAAIPQSTQEKQFSQEFRDGYSILKHYGGNGPYSERVSYGIARDPPTSCEVDQVIMVKRHGERYPSPSAGKDIEEALAKVYSINTTEYKGDLAFLNDWTYYVPNECYYNAETTSGPYAGLLDAYNHGNDYKARYGHLWNGETVVPFFSSGYGRVIETARKFGEGFFGYNYSTNAALNIISESEVMGADSLTPTCDTDNDQTTCDNLTYQLPQFKVAAARLNSQNPGMNLTASDVYNLMVMASFELNARPFSNWINAFTQDEWVSFGYVEDLNYYYCAGPGDKNMAAVGAVYANASLTLLNQGPKEAGSLFFNFAHDTNITPILAALGVLIPNEDLPLDRVAFGNPYSIGNIVPMGGHLTIERLSCQATALSDEGTYVRLVLNEAVLPFNDCTSGPGYSCPLANYTSILNKNLPDYTTTCNVSASYPQYLSFWWNYNTTTELNYRSSPIACQEGDAMD

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1235.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

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	man
拷贝数 entity_count	4

Entity 5 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	11

Entity 6 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 7 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	648

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1qfxa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.60 — Phosphoglycerate mutase-like
超家族 Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
家族 Family family	c.60.1.2 — Histidine acid phosphatase

结构域编号 domain_id	d1qfxb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.60 — Phosphoglycerate mutase-like
超家族 Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
家族 Family family	c.60.1.2 — Histidine acid phosphatase

CATH v4.4 (2 domains)

结构域编号 domain_id	1qfxA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

结构域编号 domain_id	1qfxB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

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7. 引用文献 (1)

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晶胞边长 a length_a	170.600 Å
晶胞边长 b length_b	170.600 Å
晶胞边长 c length_c	201.150 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 61 2 2
空间群编号 int_tables_number	178
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	—
R_work r_work	0.1830
R_free r_free	0.2250

fit	/app/data/saxs_computation/qf/1qfx/1qfx.fit
pddf	/app/data/pr_computation/qf/1qfx/1qfx.pr.out
profile	/app/data/saxs_computation/qf/1qfx/1qfx.dat

PH 2.5 ACID PHOSPHATASE FROM ASPERGILLUS NIGER

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution