2d81

PHB depolymerase (S39A) complexed with R3HB trimer

Method: X-RAY DIFFRACTION D_max: 56.5 Å Quality: EXCELLENT

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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2d81
沉积日期 deposition_date	2005-11-30
结构标题 title	PHB depolymerase (S39A) complexed with R3HB trimer
关键词 keywords	alpha/beta hydrolase fold, circular permutation, HYDROLASE; 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	18.82 Å
回转半径 Rg (电子) rg_electron	17.62 Å
零角强度 I(0) i0	20986600.00
分子量 molecular_weight	33974.0 kDa
排除体积 excluded_volume	41895 Å³
包络体积 envelope_volume	44592 Å³
水化壳体积 shell_volume	20446 Å³
包络直径 envelope_diameter	56.1 Å
壳层 Rg shell_rg	24.64 Å
包络 Rg envelope_rg	17.84 Å
形状 Rg shape_rg	17.60 Å
总 Rg total_rg	18.54 Å
总原子数 total_atoms	2389
残基数 n_residues	318
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	56.5 Å
Rg (实空间) rg_real	18.65 Å
Rg 误差 (实空间) rg_real_error	0.20 Å
I(0) (实空间) i0_real	2.0990e+07
I(0) 误差 (实空间) i0_real_error	2.3500e+05
Rg (倒空间) rg_reciprocal	18.68 Å
I(0) (倒空间) i0_reciprocal	20990000.0000
解质量估计 total_estimate	0.9015
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	25.5 Å
偏度 Skewness skewness	0.036
峰度 Kurtosis kurtosis	-0.501
角度范围 angular_range	— – 0.4250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5105000.0000
实空间数据点数 n_real_points	74
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.980

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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	PHB depolymerase
分子量 formula_weight	33510.0 kDa
EC 编号 ec_number	3.1.1.75
突变 mutation	S39A
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	2626

TALPAFNVNPNSVSVSGLASGGYMAAQLGVAYSDVFNVGFGVFAGGPYDCARNQYYTSCMYNGYPSITTPTANMKSWSGNQIASVANLGQRKIYMWTGSSDTTVGPNVMNQLKAQLGNFDNSANVSYVTTTGAVHTFPTDFNGAGDNSCSLSTSPYISNCNYDGAGAALKWIYGSLNARNTGTLSGSVLSFAQSGSYGANGMDTTGYLYVPQSCASGATVCSLHVALHGCLQSYSSIGSRFIQNTGYNKWADTNNMIILYPQAIPDYTIHAIWNGGVLSNPNGCWDWVGWYGSNADQIGGVQMAAIVGQVKQIVSGFQ

来源 Source

来源生物 organism	Penicillium funiculosum
NCBI 分类编号 ncbi_taxonomy_id	28572
宿主生物 host_organism	Pichia pastoris

Entity 2 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	(1R)-3-{[(1R)-3-METHOXY-1-METHYL-3-OXOPROPYL]OXY}-1-METHYL-3-OXOPROPYL (3R)-3-HYDROXYBUTANOATE
分子量 formula_weight	290.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	237

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6. 折叠分类 (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d2d81a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
家族 Family family	c.69.1.37 — PHB depolymerase-like

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7. 引用文献 (1)

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晶胞边长 a length_a	81.934 Å
晶胞边长 b length_b	48.863 Å
晶胞边长 c length_c	64.198 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.45 °
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	1.660 Å
最低分辨率 resolution_low	40.840 Å
R 因子 r_factor	0.1760
R_work r_work	0.1760
R_free r_free	0.2030

fit	/app/data/saxs_computation/d8/2d81/2d81.fit
pddf	/app/data/pr_computation/d8/2d81/2d81.pr.out
profile	/app/data/saxs_computation/d8/2d81/2d81.dat