1kbp

KIDNEY BEAN PURPLE ACID PHOSPHATASE

Method: X-RAY DIFFRACTION D_max: 167.0 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	1kbp
沉积日期 deposition_date	1995-02-20
结构标题 title	KIDNEY BEAN PURPLE ACID PHOSPHATASE
关键词 keywords	PURPLE ACID PHOSPHATASE, HYDROLASE (PHOSPHORIC MONOESTER); HYDROLASE (PHOSPHORIC MONOESTER)
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	48.53 Å
回转半径 Rg (电子) rg_electron	48.75 Å
零角强度 I(0) i0	588570000.00
分子量 molecular_weight	201580.0 kDa
排除体积 excluded_volume	251370 Å³
包络体积 envelope_volume	321970 Å³
水化壳体积 shell_volume	55501 Å³
包络直径 envelope_diameter	171.3 Å
壳层 Rg shell_rg	52.03 Å
包络 Rg envelope_rg	48.00 Å
形状 Rg shape_rg	48.73 Å
总 Rg total_rg	48.93 Å
总原子数 total_atoms	14264
残基数 n_residues	1696
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	167.0 Å
Rg (实空间) rg_real	48.82 Å
Rg 误差 (实空间) rg_real_error	2.05 Å
I(0) (实空间) i0_real	5.8860e+08
I(0) 误差 (实空间) i0_real_error	1.1610e+07
Rg (倒空间) rg_reciprocal	48.53 Å
I(0) (倒空间) i0_reciprocal	588300000.0000
解质量估计 total_estimate	0.8451
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	62.6 Å
偏度 Skewness skewness	0.348
峰度 Kurtosis kurtosis	-0.567
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	41110000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.829; Smooth: 0.680

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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	PURPLE ACID PHOSPHATASE
分子量 formula_weight	50304.3 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	14334

FVRKTNKNRDMPLDSDVFRVPPGYNAPQQVHITQGDLVGRAMIISWVTMDEPGSSAVRYWSEKNGRKRIAKGKMSTYRFFNYSSGFIHHTTIRKLKYNTKYYYEVGLRNTTRRFSFITPPQTGLDVPYTFGLIGDLGQSFDSNTTLSHYELSPKKGQTVLFVGDLSYADRYPNHDNVRWDTWGRFTERSVAYQPWIWTAGNHEIEFAPEINETEPFKPFSYRYHVPYEASQSTSPFWYSIKRASAHIIVLSSYSAYGRGTPQYTWLKKELRKVKRSETPWLIVLMHSPLYNSYNHHFMEGEAMRTKFEAWFVKYKVDVVFAGHVHAYERSERVSNIAYKITDGLCTPVKDQSAPVYITIGDAGNYGVIDSNMIQPQPEYSAFREASFGHGMFDIKNRTHAHFSWNRNQDGVAVEADSVWFFNRHWYPVDDST

Entity 2 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	20

Entity 3 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	70

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1kbpa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.12 — Purple acid phosphatase, N-terminal domain
家族 Family family	b.1.12.1 — Purple acid phosphatase, N-terminal domain

结构域编号 domain_id	d1kbpa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.159 — Metallo-dependent phosphatases
超家族 Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
家族 Family family	d.159.1.1 — Purple acid phosphatase-like

结构域编号 domain_id	d1kbpb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.12 — Purple acid phosphatase, N-terminal domain
家族 Family family	b.1.12.1 — Purple acid phosphatase, N-terminal domain

结构域编号 domain_id	d1kbpb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.159 — Metallo-dependent phosphatases
超家族 Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
家族 Family family	d.159.1.1 — Purple acid phosphatase-like

结构域编号 domain_id	d1kbpc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.12 — Purple acid phosphatase, N-terminal domain
家族 Family family	b.1.12.1 — Purple acid phosphatase, N-terminal domain

结构域编号 domain_id	d1kbpc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.159 — Metallo-dependent phosphatases
超家族 Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
家族 Family family	d.159.1.1 — Purple acid phosphatase-like

结构域编号 domain_id	d1kbpd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.12 — Purple acid phosphatase, N-terminal domain
家族 Family family	b.1.12.1 — Purple acid phosphatase, N-terminal domain

结构域编号 domain_id	d1kbpd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.159 — Metallo-dependent phosphatases
超家族 Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
家族 Family family	d.159.1.1 — Purple acid phosphatase-like

CATH v4.4 (8 domains)

结构域编号 domain_id	1kbpA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	380 — Purple acid phosphatase-like, N-terminal

结构域编号 domain_id	1kbpA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Metallo-dependent phosphatases

结构域编号 domain_id	1kbpB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	380 — Purple acid phosphatase-like, N-terminal

结构域编号 domain_id	1kbpB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Metallo-dependent phosphatases

结构域编号 domain_id	1kbpC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	380 — Purple acid phosphatase-like, N-terminal

结构域编号 domain_id	1kbpC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Metallo-dependent phosphatases

结构域编号 domain_id	1kbpD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	380 — Purple acid phosphatase-like, N-terminal

结构域编号 domain_id	1kbpD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Metallo-dependent phosphatases

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7. 引用文献 (2)

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晶胞边长 a length_a	132.700 Å
晶胞边长 b length_b	347.300 Å
晶胞边长 c length_c	128.700 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	32

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.650 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2330

fit	/app/data/saxs_computation/kb/1kbp/1kbp.fit
pddf	/app/data/pr_computation/kb/1kbp/1kbp.pr.out
profile	/app/data/saxs_computation/kb/1kbp/1kbp.dat