SAXSdb — 1pzx

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1pzx
沉积日期 deposition_date	2003-07-14
结构标题 title	Hypothetical protein APC36103 from Bacillus stearothermophilus: a lipid binding protein
关键词 keywords	;Structural genomics, Two domains containing mixed alpha/beta structures, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, Lipid Binding Protein ;; LIPID BINDING PROTEIN
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	29.37 Å
回转半径 Rg (电子) rg_electron	28.75 Å
零角强度 I(0) i0	63521400.00
分子量 molecular_weight	64105.0 kDa
排除体积 excluded_volume	80895 Å³
包络体积 envelope_volume	98213 Å³
水化壳体积 shell_volume	28829 Å³
包络直径 envelope_diameter	100.2 Å
壳层 Rg shell_rg	35.46 Å
包络 Rg envelope_rg	28.55 Å
形状 Rg shape_rg	28.74 Å
总 Rg total_rg	29.46 Å
总原子数 total_atoms	4503
残基数 n_residues	566
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	95.2 Å
Rg (实空间) rg_real	29.43 Å
Rg 误差 (实空间) rg_real_error	0.67 Å
I(0) (实空间) i0_real	6.3520e+07
I(0) 误差 (实空间) i0_real_error	9.9850e+05
Rg (倒空间) rg_reciprocal	29.41 Å
I(0) (倒空间) i0_reciprocal	63520000.0000
解质量估计 total_estimate	0.8924
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	28.2 Å
偏度 Skewness skewness	0.344
峰度 Kurtosis kurtosis	-0.536
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	17640000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.912

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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	Hypothetical protein APC36103
分子量 formula_weight	32400.3 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	4850

NAMPIEIITDSGADLPQSYIREHRIAFLPLVVHWNGQDYKDGITIEPKQVYDAMRQGHTVKTAQPSPLAMKELFLPYAKENRPCLYIAFSSKLSGTYQTAMAVRSELLDEYPEFRLTIIDSKCASLGQGLAVMKAVELAKQNTPYNLLCETIESYCRHMEHIFTVDNLDYLARGGRISKTAAAFGGLLNIKPLLHVEDGALIPLEKWRGRKKVLKRMVELMGERGDDLQKQTIGISHADDEETALELKQMIEETHGCTRFFLSDIGSAIGAHAGPGTIALFFLNKYIEI

来源 Source

来源生物 organism	Geobacillus stearothermophilus
NCBI 分类编号 ncbi_taxonomy_id	1422
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	PALMITIC ACID
分子量 formula_weight	256.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	347

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1pzxa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.119 — DAK1/DegV-like
超家族 Superfamily superfamily	c.119.1 — DAK1/DegV-like
家族 Family family	c.119.1.1 — DegV-like

结构域编号 domain_id	d1pzxb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.119 — DAK1/DegV-like
超家族 Superfamily superfamily	c.119.1 — DAK1/DegV-like
家族 Family family	c.119.1.1 — DegV-like

CATH v4.4 (6 domains)

结构域编号 domain_id	1pzxA01
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	10440 — Dihydroxyacetone kinase; domain 1

结构域编号 domain_id	1pzxA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily	50 — DegV, N-terminal domain, peripheral subdomain

结构域编号 domain_id	1pzxA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1180 — Hypothetical Protein Tm841; Chain: A;domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1pzxB01
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	10440 — Dihydroxyacetone kinase; domain 1

结构域编号 domain_id	1pzxB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily	50 — DegV, N-terminal domain, peripheral subdomain

结构域编号 domain_id	1pzxB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1180 — Hypothetical Protein Tm841; Chain: A;domain 3
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	65.980 Å
晶胞边长 b length_b	187.390 Å
晶胞边长 c length_c	53.290 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 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	34.540 Å
R 因子 r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2520

fit	/app/data/saxs_computation/pz/1pzx/1pzx.fit
pddf	/app/data/pr_computation/pz/1pzx/1pzx.pr.out
profile	/app/data/saxs_computation/pz/1pzx/1pzx.dat

Hypothetical protein APC36103 from Bacillus stearothermophilus: a lipid binding protein

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