SAXSdb — 2gju

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gju
沉积日期 deposition_date	2006-03-31
结构标题 title	Crystal structure of hypothetical protein PH1004 from Pyrococcus horikoshii OT3
关键词 keywords	;BETA BARREL, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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	42.75 Å
回转半径 Rg (电子) rg_electron	42.61 Å
零角强度 I(0) i0	174824000.00
分子量 molecular_weight	115290.0 kDa
排除体积 excluded_volume	147240 Å³
包络体积 envelope_volume	200910 Å³
水化壳体积 shell_volume	40529 Å³
包络直径 envelope_diameter	142.5 Å
壳层 Rg shell_rg	46.02 Å
包络 Rg envelope_rg	41.45 Å
形状 Rg shape_rg	42.61 Å
总 Rg total_rg	42.78 Å
总原子数 total_atoms	8127
残基数 n_residues	1008
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	144.9 Å
Rg (实空间) rg_real	42.91 Å
Rg 误差 (实空间) rg_real_error	1.72 Å
I(0) (实空间) i0_real	1.7480e+08
I(0) 误差 (实空间) i0_real_error	3.1310e+06
Rg (倒空间) rg_reciprocal	42.75 Å
I(0) (倒空间) i0_reciprocal	174800000.0000
解质量估计 total_estimate	0.8410
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	31.3 Å
偏度 Skewness skewness	0.265
峰度 Kurtosis kurtosis	-0.740
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	20810000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.770; Smooth: 0.882

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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 (4)

Entity 1 polymer

描述 description	252aa long hypothetical protein
分子量 formula_weight	28678.3 kDa
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	9166

MVYVAVLANIAGNFPALTAALEKIEELKEEGYEIEKYYILGNIVGLFPYPREVIEAIKNLAKTSNVKVIRGKYDQLIAMSDPHAGDPKYIDKLEIPDHLKATLKYTWEKLGHEGREYLRDLPIYLVDKIGKNEIFGVYGSPVNPFDGEILPDQPTSYYEAIMRPVKEYEMLLVASPRYPLDAMTMYGRVVCPGSIGFPPAREHKATFALVDAETLKVKFIEVEYDKKIIEDRIKLEKLPEEVIKILYHGGKA

来源 Source

来源生物 organism	Pyrococcus horikoshii
NCBI 分类编号 ncbi_taxonomy_id	70601
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 4 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	1039

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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	d2gjua_
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.159.1.5 — Phosphoesterase-related

结构域编号 domain_id	d2gjub_
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.159.1.5 — Phosphoesterase-related

结构域编号 domain_id	d2gjuc_
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.159.1.5 — Phosphoesterase-related

结构域编号 domain_id	d2gjud_
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.159.1.5 — Phosphoesterase-related

CATH v4.4 (4 domains)

结构域编号 domain_id	2gjuA00
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	2gjuB00
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	2gjuC00
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	2gjuD00
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 (1)

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晶胞边长 a length_a	99.742 Å
晶胞边长 b length_b	129.571 Å
晶胞边长 c length_c	113.557 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	104.46 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	39.430 Å
R 因子 r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2140

fit	/app/data/saxs_computation/gj/2gju/2gju.fit
pddf	/app/data/pr_computation/gj/2gju/2gju.pr.out
profile	/app/data/saxs_computation/gj/2gju/2gju.dat

Crystal structure of hypothetical protein PH1004 from Pyrococcus horikoshii OT3

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction