SAXSdb — 2j9p

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2j9p
沉积日期 deposition_date	2006-11-15
结构标题 title	Crystal structure of the Bacillus subtilis PBP4a, and its complex with a peptidoglycan mimetic peptide.
关键词 keywords	;D-ALA-D-ALA- CARBOXYPEPTIDASE, PEPTIDOGLYCAN SYNTHESIS, PENICILLIN-BINDING PROTEIN, PEPTIDOGLYCAN, CELL DIVISION, BACILLUS SUBTILIS, CELL WALL, HYDROLASE, CELL SHAPE, CELL CYCLE ;; 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	65.71 Å
回转半径 Rg (电子) rg_electron	66.45 Å
零角强度 I(0) i0	138505000.00
分子量 molecular_weight	99072.0 kDa
排除体积 excluded_volume	123970 Å³
包络体积 envelope_volume	226070 Å³
水化壳体积 shell_volume	28601 Å³
包络直径 envelope_diameter	188.3 Å
壳层 Rg shell_rg	73.23 Å
包络 Rg envelope_rg	59.49 Å
形状 Rg shape_rg	66.44 Å
总 Rg total_rg	66.60 Å
总原子数 total_atoms	6966
残基数 n_residues	916
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	203.8 Å
Rg (实空间) rg_real	66.70 Å
Rg 误差 (实空间) rg_real_error	2.32 Å
I(0) (实空间) i0_real	1.3850e+08
I(0) 误差 (实空间) i0_real_error	3.1330e+06
Rg (倒空间) rg_reciprocal	64.56 Å
I(0) (倒空间) i0_reciprocal	137900000.0000
解质量估计 total_estimate	0.5417
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	25.5 Å
偏度 Skewness skewness	0.064
峰度 Kurtosis kurtosis	-1.663
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2404000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.000; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.039; Smooth: 0.000

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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	D-alanyl-D-alanine carboxypeptidase DacC
分子量 formula_weight	49762.9 kDa
EC 编号 ec_number	3.4.16.4
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	6966

AEKQDALSGQIDKILADHPALEGAMAGITVRSAETGAVLYEHSGDTRMRPASSLKLLTAAAALSVLGENYSFTTEVRTDGTLKGKKLNGNLYLKGKGDPTLLPSDFDKMAEILKHSGVKVIKGNLIGDDTWHDDMRLSPDMPWSDEYTYYGAPISALTASPNEDYDAGTVIVEVTPNQKEGEEPAVSVSPKTDYITIKNDAKTTAAGSEKDLTIEREHGTNTITIEGSVPVDANKTKEWISVWEPAGYALDLFKQSLKKQGITVKGDIKTGEAPSSSDVLLSHRSMPLSKLFVPFMKLSNNGHAEVLVKEMGKVKKGEGSWEKGLEVLNSTLPEFGVDSKSLVLRDGSGISHIDAVSSDQLSQLLYDIQDQSWFSAYLNSLPVAGNPDRMVGGTLRNRMKGTPAQGKVRAKTGSLSTVSSLSGYAETKSGKKLVFSILLNGLIDEEDGKDIEDQIAVILANQ

来源 Source

来源生物 organism	Bacillus subtilis
NCBI 分类编号 ncbi_taxonomy_id	224308
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	(2R)-2-AMINO-7-{[(1R)-1-CARBOXYETHYL]AMINO}-7-OXOHEPTANOIC ACID
分子量 formula_weight	246.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	D-ALANINE
分子量 formula_weight	89.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2j9pa1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.3 — beta-lactamase/transpeptidase-like
超家族 Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
家族 Family family	e.3.1.3 — Dac-like

结构域编号 domain_id	d2j9pb1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.3 — beta-lactamase/transpeptidase-like
超家族 Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
家族 Family family	e.3.1.3 — Dac-like

CATH v4.4 (4 domains)

结构域编号 domain_id	2j9pA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	710 — Beta-lactamase
同源超家族 H-superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

结构域编号 domain_id	2j9pA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
同源超家族 H-superfamily homologous superfamily	20 — D-Ala-D-Ala carboxypeptidase C, peptidase S13

结构域编号 domain_id	2j9pB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	710 — Beta-lactamase
同源超家族 H-superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

结构域编号 domain_id	2j9pB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
同源超家族 H-superfamily homologous superfamily	20 — D-Ala-D-Ala carboxypeptidase C, peptidase S13

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7. 引用文献 (1)

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晶胞边长 a length_a	73.859 Å
晶胞边长 b length_b	77.586 Å
晶胞边长 c length_c	164.739 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	2.800 Å
最低分辨率 resolution_low	19.900 Å
R 因子 r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2900

fit	/app/data/saxs_computation/j9/2j9p/2j9p.fit
pddf	/app/data/pr_computation/j9/2j9p/2j9p.pr.out
profile	/app/data/saxs_computation/j9/2j9p/2j9p.dat

Crystal structure of the Bacillus subtilis PBP4a, and its complex with a peptidoglycan mimetic peptide.

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