1z8l

Crystal structure of prostate-specific membrane antigen, a tumor marker and peptidase

Method: X-RAY DIFFRACTION D_max: 169.0 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	1z8l
沉积日期 deposition_date	2005-03-30
结构标题 title	Crystal structure of prostate-specific membrane antigen, a tumor marker and peptidase
关键词 keywords	Dimeric protein with three domains of type A+B, 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	49.64 Å
回转半径 Rg (电子) rg_electron	49.44 Å
零角强度 I(0) i0	1451800000.00
分子量 molecular_weight	323240.0 kDa
排除体积 excluded_volume	405880 Å³
包络体积 envelope_volume	521140 Å³
水化壳体积 shell_volume	86662 Å³
包络直径 envelope_diameter	174.9 Å
壳层 Rg shell_rg	53.36 Å
包络 Rg envelope_rg	49.60 Å
形状 Rg shape_rg	49.44 Å
总 Rg total_rg	49.57 Å
总原子数 total_atoms	22824
残基数 n_residues	2780
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	169.0 Å
Rg (实空间) rg_real	49.68 Å
Rg 误差 (实空间) rg_real_error	1.53 Å
I(0) (实空间) i0_real	1.4520e+09
I(0) 误差 (实空间) i0_real_error	2.4860e+07
Rg (倒空间) rg_reciprocal	49.64 Å
I(0) (倒空间) i0_reciprocal	1452000000.0000
解质量估计 total_estimate	0.8773
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	52.8 Å
偏度 Skewness skewness	0.319
峰度 Kurtosis kurtosis	-0.455
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	283200000.0000
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: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.813

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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	Glutamate carboxypeptidase II
分子量 formula_weight	78341.4 kDa
EC 编号 ec_number	3.4.17.21
来源方法 src_method	man
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	22836

HNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGLDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENVSDIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTRIYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGTLKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNKFSGYPLYHSVYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFDKSNPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606

Entity 2 branched

描述 description	2-acetamido-2-deoxy-alpha-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	8

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	man
拷贝数 entity_count	12

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	8

Entity 5 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	8

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	12

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1z8la1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.48 — N-cbl like
超家族 Superfamily superfamily	a.48.2 — Transferrin receptor-like dimerisation domain
家族 Family family	a.48.2.1 — Transferrin receptor-like dimerisation domain

结构域编号 domain_id	d1z8la2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.4 — PA domain
家族 Family family	c.8.4.1 — PA domain

结构域编号 domain_id	d1z8la3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
家族 Family family	c.56.5.5 — FolH catalytic domain-like

结构域编号 domain_id	d1z8lb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.48 — N-cbl like
超家族 Superfamily superfamily	a.48.2 — Transferrin receptor-like dimerisation domain
家族 Family family	a.48.2.1 — Transferrin receptor-like dimerisation domain

结构域编号 domain_id	d1z8lb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.4 — PA domain
家族 Family family	c.8.4.1 — PA domain

结构域编号 domain_id	d1z8lb3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
家族 Family family	c.56.5.5 — FolH catalytic domain-like

结构域编号 domain_id	d1z8lc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.48 — N-cbl like
超家族 Superfamily superfamily	a.48.2 — Transferrin receptor-like dimerisation domain
家族 Family family	a.48.2.1 — Transferrin receptor-like dimerisation domain

结构域编号 domain_id	d1z8lc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.4 — PA domain
家族 Family family	c.8.4.1 — PA domain

结构域编号 domain_id	d1z8lc3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
家族 Family family	c.56.5.5 — FolH catalytic domain-like

结构域编号 domain_id	d1z8ld1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.48 — N-cbl like
超家族 Superfamily superfamily	a.48.2 — Transferrin receptor-like dimerisation domain
家族 Family family	a.48.2.1 — Transferrin receptor-like dimerisation domain

结构域编号 domain_id	d1z8ld2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.4 — PA domain
家族 Family family	c.8.4.1 — PA domain

结构域编号 domain_id	d1z8ld3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
家族 Family family	c.56.5.5 — FolH catalytic domain-like

CATH v4.4 (12 domains)

结构域编号 domain_id	1z8lA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	1z8lA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	30 — Glucose Oxidase; domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1z8lA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	930 — Transcription Elongation Factor S-II; Chain A
同源超家族 H-superfamily homologous superfamily	40 — Transferrin receptor-like, dimerisation domain

结构域编号 domain_id	1z8lB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	1z8lB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	30 — Glucose Oxidase; domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1z8lB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	930 — Transcription Elongation Factor S-II; Chain A
同源超家族 H-superfamily homologous superfamily	40 — Transferrin receptor-like, dimerisation domain

结构域编号 domain_id	1z8lC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	1z8lC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	30 — Glucose Oxidase; domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1z8lC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	930 — Transcription Elongation Factor S-II; Chain A
同源超家族 H-superfamily homologous superfamily	40 — Transferrin receptor-like, dimerisation domain

结构域编号 domain_id	1z8lD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	1z8lD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	30 — Glucose Oxidase; domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1z8lD03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	930 — Transcription Elongation Factor S-II; Chain A
同源超家族 H-superfamily homologous superfamily	40 — Transferrin receptor-like, dimerisation domain

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7. 引用文献 (1)

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晶胞边长 a length_a	74.865 Å
晶胞边长 b length_b	157.765 Å
晶胞边长 c length_c	133.839 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	93.24 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	3.500 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.2520
R_free r_free	0.2840

fit	/app/data/saxs_computation/z8/1z8l/1z8l.fit
pddf	/app/data/pr_computation/z8/1z8l/1z8l.pr.out
profile	/app/data/saxs_computation/z8/1z8l/1z8l.dat