SAXSdb — 2hqy

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2hqy
沉积日期 deposition_date	2006-07-19
结构标题 title	Crystal Structure of Conserved Protein of Unknown Function from Bacteroides thetaiotaomicron VPI-5482
关键词 keywords	;conserved hypothetical protein, MCSG, PSI2, MAD, Structural Genomics, Protein Structure Initiative, Midwest Center for Structural Genomics, 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	27.78 Å
回转半径 Rg (电子) rg_electron	26.92 Å
零角强度 I(0) i0	79588400.00
分子量 molecular_weight	69513.0 kDa
排除体积 excluded_volume	86797 Å³
包络体积 envelope_volume	106470 Å³
水化壳体积 shell_volume	33102 Å³
包络直径 envelope_diameter	96.5 Å
壳层 Rg shell_rg	34.05 Å
包络 Rg envelope_rg	26.84 Å
形状 Rg shape_rg	26.91 Å
总 Rg total_rg	27.67 Å
总原子数 total_atoms	4884
残基数 n_residues	594
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	91.0 Å
Rg (实空间) rg_real	27.75 Å
Rg 误差 (实空间) rg_real_error	0.54 Å
I(0) (实空间) i0_real	7.9590e+07
I(0) 误差 (实空间) i0_real_error	1.0430e+06
Rg (倒空间) rg_reciprocal	27.76 Å
I(0) (倒空间) i0_reciprocal	79590000.0000
解质量估计 total_estimate	0.8921
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	30.3 Å
偏度 Skewness skewness	0.315
峰度 Kurtosis kurtosis	-0.363
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	20310000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.954

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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 (3)

Entity 1 polymer

描述 description	conserved hypothetical protein
分子量 formula_weight	35483.5 kDa
来源方法 src_method	man
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	5595

MIPFKDITLADRDTITAFTMKSDRRNCDLSFSNLCSWRFLYDTQFAVIDDFLVFKFWAGEQLAYMMPVGNGDLKAVLRKLIEDADKEKHNFCMLGVCSNMRADLEAILPERFIFTEDRAYADYIYLRSDLATLKGKKFQAKRNHINRFRNTYPDYEYTPITPDRIQECLDLEAEWCKVNNCDQQEGTGNERRALIYALHNFEALGLTGGILHVNGKIVAFTFGMPINHETFGVHVEKADTSIDGAYAMINYEFANRIPEQYIYINREEDLGIEGLRKAKLSYQPVTILEKYMACLKDHPMDMVRW

来源 Source

来源生物 organism	Bacteroides thetaiotaomicron
NCBI 分类编号 ncbi_taxonomy_id	226186
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	COENZYME A
分子量 formula_weight	767.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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	613

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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	d2hqya1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
超家族 Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
家族 Family family	d.108.1.4 — FemXAB nonribosomal peptidyltransferases

结构域编号 domain_id	d2hqya2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
超家族 Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
家族 Family family	d.108.1.4 — FemXAB nonribosomal peptidyltransferases

结构域编号 domain_id	d2hqyb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
超家族 Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
家族 Family family	d.108.1.4 — FemXAB nonribosomal peptidyltransferases

结构域编号 domain_id	d2hqyb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
超家族 Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
家族 Family family	d.108.1.4 — FemXAB nonribosomal peptidyltransferases

CATH v4.4 (4 domains)

结构域编号 domain_id	2hqyA01
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	30 — Gcn5-related N-acetyltransferase (GNAT)

结构域编号 domain_id	2hqyA02
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	30 — Gcn5-related N-acetyltransferase (GNAT)

结构域编号 domain_id	2hqyB01
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	30 — Gcn5-related N-acetyltransferase (GNAT)

结构域编号 domain_id	2hqyB02
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	30 — Gcn5-related N-acetyltransferase (GNAT)

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7. 引用文献 (1)

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晶胞边长 a length_a	66.468 Å
晶胞边长 b length_b	81.879 Å
晶胞边长 c length_c	138.449 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	8

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	1.800 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.1774
R_work r_work	0.1756
R_free r_free	0.2112

fit	/app/data/saxs_computation/hq/2hqy/2hqy.fit
pddf	/app/data/pr_computation/hq/2hqy/2hqy.pr.out
profile	/app/data/saxs_computation/hq/2hqy/2hqy.dat

Crystal Structure of Conserved Protein of Unknown Function from Bacteroides thetaiotaomicron VPI-5482

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