2bib

Crystal structure of the complete modular teichioic acid phosphorylcholine esterase Pce (CbpE) from Streptococcus pneumoniae

Method: X-RAY DIFFRACTION D_max: 146.5 Å Quality: REASONABLE

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2bib
沉积日期 deposition_date	2005-01-20
结构标题 title	Crystal structure of the complete modular teichioic acid phosphorylcholine esterase Pce (CbpE) from Streptococcus pneumoniae
关键词 keywords	CHOLINE-BINDING PROTEIN, CBPE, PCE, PHOSPHORYLCHOLINE ESTERASE, HYDROLASE, TEICHOIC ACID; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	36.99 Å
回转半径 Rg (电子) rg_electron	38.64 Å
零角强度 I(0) i0	65782900.00
分子量 molecular_weight	64487.0 kDa
排除体积 excluded_volume	80326 Å³
包络体积 envelope_volume	105970 Å³
水化壳体积 shell_volume	26698 Å³
包络直径 envelope_diameter	148.4 Å
壳层 Rg shell_rg	37.44 Å
包络 Rg envelope_rg	39.64 Å
形状 Rg shape_rg	38.64 Å
总 Rg total_rg	38.55 Å
总原子数 total_atoms	4553
残基数 n_residues	541
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

▼

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

最大尺寸 Dmax dmax	146.5 Å
Rg (实空间) rg_real	38.16 Å
Rg 误差 (实空间) rg_real_error	2.32 Å
I(0) (实空间) i0_real	6.5780e+07
I(0) 误差 (实空间) i0_real_error	1.3060e+06
Rg (倒空间) rg_reciprocal	37.43 Å
I(0) (倒空间) i0_reciprocal	65740000.0000
解质量估计 total_estimate	0.6304
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	27.3 Å
偏度 Skewness skewness	0.813
峰度 Kurtosis kurtosis	-0.167
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7845000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.083; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.006; Smooth: 0.936

▶

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

▶

5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	TEICHOIC ACID PHOSPHORYLCHOLINE ESTERASE/ CHOLINE BINDING PROTEIN
分子量 formula_weight	63427.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4985

QESSGNKIHFINVQEGGSDAIILESNGHFAMVDTGEDYDFPDGSDSRYPWREGIETSYKHVLTDRVFRRLKELSVQKLDFILVTHTHSDHIGNVDELLSTYPVDRVYLKKYSDSRITNSERLWDNLYGYDKVLQTATETGVSVIQNITQGDAHFQFGDMDIQLYNYENETDSSGELKKIWDDNSNSLISVVKVNGKKIYLGGDLDNVHGAEDKYGPLIGKVDLMKFNHHHDTNKSNTKDFIKNLSPSLIVQTSDSLPWKNGVDSEYVNWLKERGIERINAASKDYDATVFDIRKDGFVNISTSYKPIPSFQAGWHKSAYGNWWYQAPDSTGEYAVGWNEIEGEWYYFNQTGILLQNQWKKWNNHWFYLTDSGASAKNWKKIDGIWYYFNKENQMEIGWVQDKEQWYYLDVDGSMKTGWLQYMGQWYYFAPSGEMKMGWVKDKETWYYMDSTGVMKTGEIEVAGQHYYLEDSGAMKQGWHKKANDWYFYKTDGSRAVGWIKDKDKWYFLKENGQLLVNGKTPEGYTVDSSGAWLVDVSIEKSATIKTT

来源 Source

来源生物 organism	STREPTOCOCCUS PNEUMONIAE
NCBI 分类编号 ncbi_taxonomy_id	1313
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	PHOSPHOCHOLINE
分子量 formula_weight	184.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
分子量 formula_weight	209.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

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	2

Entity 5 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	432

▼

6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2biba1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.109 — beta-hairpin stack
超家族 Superfamily superfamily	b.109.1 — Cell wall binding repeat
家族 Family family	b.109.1.1 — Cell wall binding repeat

结构域编号 domain_id	d2biba2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
超家族 Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
家族 Family family	d.157.1.8 — Pce catalytic domain-like

CATH v4.4 (1 domains)

结构域编号 domain_id	2bibA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	15 — Metallo-beta-lactamase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	173.490 Å
晶胞边长 b length_b	58.120 Å
晶胞边长 c length_c	68.650 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	108.29 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	1.920 Å
最低分辨率 resolution_low	27.520 Å
R 因子 r_factor	0.1970
R_work r_work	0.1940
R_free r_free	0.2330

fit	/app/data/saxs_computation/bi/2bib/2bib.fit
pddf	/app/data/pr_computation/bi/2bib/2bib.pr.out
profile	/app/data/saxs_computation/bi/2bib/2bib.dat