SAXSdb — 2hpa

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2hpa
沉积日期 deposition_date	1998-09-11
结构标题 title	STRUCTURAL ORIGINS OF L(+)-TARTRATE INHIBITION OF HUMAN PROSTATIC ACID PHOSPHATASE
关键词 keywords	ACID PHOSPHATASE, N-PROPYLTARTRAMATE, 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	37.31 Å
回转半径 Rg (电子) rg_electron	37.02 Å
零角强度 I(0) i0	376795000.00
分子量 molecular_weight	162000.0 kDa
排除体积 excluded_volume	204250 Å³
包络体积 envelope_volume	250060 Å³
水化壳体积 shell_volume	56600 Å³
包络直径 envelope_diameter	139.7 Å
壳层 Rg shell_rg	42.85 Å
包络 Rg envelope_rg	36.84 Å
形状 Rg shape_rg	37.01 Å
总 Rg total_rg	37.42 Å
总原子数 total_atoms	11416
残基数 n_residues	1368
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	129.7 Å
Rg (实空间) rg_real	37.35 Å
Rg 误差 (实空间) rg_real_error	1.08 Å
I(0) (实空间) i0_real	3.7680e+08
I(0) 误差 (实空间) i0_real_error	6.1180e+06
Rg (倒空间) rg_reciprocal	37.32 Å
I(0) (倒空间) i0_reciprocal	376800000.0000
解质量估计 total_estimate	0.8686
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	43.2 Å
偏度 Skewness skewness	0.422
峰度 Kurtosis kurtosis	-0.135
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	96880000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.946

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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 (ACID PHOSPHATASE)
分子量 formula_weight	39776.4 kDa
EC 编号 ec_number	3.1.3.2
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	11766

KELKFVTLVFRHGDRSPIDTFPTDPIKESSWPQGFGQLTQLGMEQHYELGEYIRKRYRKFLNESYKHEQVYIRSTDVDRTLMSAMTNLAALFPPEGVSIWNPILLWQPIPVHTVPLSEDQLLYLPFRNCPRFQELESETLKSEEFQKRLHPYKDFIATLGKLSGLHGQDLFGIWSKVYDPLYCESVHNFTLPSWATEDTMTKLRELSELSLLSLYGIHKQKEKSRLQGGVLVNEILNHMKRATQIPSYKKLIMYSAHDTTVSGLQMALDVYNGLLPPYASCHLTELYFEKGEYFVEMYYRNETQHEPYPLMLPGCSPSCPLERFAELVGPVIPQDWSTECMT

Entity 2 branched

描述 description	alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	545.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 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	syn
拷贝数 entity_count	1

Entity 4 branched

描述 description	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	586.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	5

Entity 6 non-polymer

描述 description	N-PROPYL-TARTRAMIC ACID
分子量 formula_weight	191.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	350

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2hpaa_
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	d2hpab_
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	d2hpac_
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	d2hpad_
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 (4 domains)

结构域编号 domain_id	2hpaA00
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	2hpaB00
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	2hpaC00
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	2hpaD00
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 (2)

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晶胞边长 a length_a	119.860 Å
晶胞边长 b length_b	202.680 Å
晶胞边长 c length_c	71.110 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	16

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	2.900 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.3080

fit	/app/data/saxs_computation/hp/2hpa/2hpa.fit
pddf	/app/data/pr_computation/hp/2hpa/2hpa.pr.out
profile	/app/data/saxs_computation/hp/2hpa/2hpa.dat

STRUCTURAL ORIGINS OF L(+)-TARTRATE INHIBITION OF HUMAN PROSTATIC ACID PHOSPHATASE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution