SAXSdb — 2bkk

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2bkk
沉积日期 deposition_date	2005-02-16
结构标题 title	;Crystal structure of Aminoglycoside Phosphotransferase APH(3')-IIIa in complex with the inhibitor AR_3a ;
关键词 keywords	;TRANSFERASE/PEPTIDE, TRANSFERASE-DESIGNED PROTEIN COMPLEX, ANKYRIN REPEAT, CO-CRYSTALLIZATION, INHIBITOR DESIGN, DRUG DESIGN, ENZYME INHIBITION, KINASE INHIBITION, DESIGNED REPEAT PROTEIN, ANTIBIOTIC RESISTANCE, ATP-BINDING, KINASE, PLASMID, TRANSFERASE, TRANSFERASE-PEPTIDE complex ;; TRANSFERASE/PEPTIDE
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	33.72 Å
回转半径 Rg (电子) rg_electron	33.33 Å
零角强度 I(0) i0	139573000.00
分子量 molecular_weight	94440.0 kDa
排除体积 excluded_volume	118030 Å³
包络体积 envelope_volume	156640 Å³
水化壳体积 shell_volume	40138 Å³
包络直径 envelope_diameter	113.1 Å
壳层 Rg shell_rg	39.47 Å
包络 Rg envelope_rg	32.81 Å
形状 Rg shape_rg	33.30 Å
总 Rg total_rg	33.91 Å
总原子数 total_atoms	6653
残基数 n_residues	822
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	108.6 Å
Rg (实空间) rg_real	33.70 Å
Rg 误差 (实空间) rg_real_error	1.11 Å
I(0) (实空间) i0_real	1.3960e+08
I(0) 误差 (实空间) i0_real_error	2.2940e+06
Rg (倒空间) rg_reciprocal	33.72 Å
I(0) (倒空间) i0_reciprocal	139600000.0000
解质量估计 total_estimate	0.9010
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	41.6 Å
偏度 Skewness skewness	0.269
峰度 Kurtosis kurtosis	-0.510
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	23450000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.911

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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 (5)

Entity 1 polymer

描述 description	;AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE ;
分子量 formula_weight	30979.9 kDa
EC 编号 ec_number	2.7.1.95
突变 mutation	YES
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,C
原子数 atom_count	7000

MAKMRISPELKKLIEKYRSVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDSENWEEDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVELFFDLLGIKPDWEKIKYYILLDELF

来源 Source

来源生物 organism	ENTEROCOCCUS FAECALIS
NCBI 分类编号 ncbi_taxonomy_id	1351
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	DESIGNED ANKYRIN REPEAT INHIBITOR AR_3A
分子量 formula_weight	18602.8 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	B,D

MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNANDWFGITPLHLVVNNGHLEIIEVLLKYAADVNASDKSGWTPLHLAAYRGHLEIVEVLLKYGADVNAMDYQGYTPLHLAAEDGHLEIVEVLLKYGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN

来源 Source

来源生物 organism	SYNTHETIC CONSTRUCT
NCBI 分类编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 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	d2bkka_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
家族 Family family	d.144.1.6 — APH phosphotransferases

结构域编号 domain_id	d2bkkc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
家族 Family family	d.144.1.6 — APH phosphotransferases

CATH v4.4 (6 domains)

结构域编号 domain_id	2bkkA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	2bkkA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1200 — Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminoglycoside phosphotransferase (APH), C-terminal lobe

结构域编号 domain_id	2bkkB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

结构域编号 domain_id	2bkkC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	2bkkC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1200 — Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminoglycoside phosphotransferase (APH), C-terminal lobe

结构域编号 domain_id	2bkkD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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7. 引用文献 (1)

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晶胞边长 a length_a	59.670 Å
晶胞边长 b length_b	98.082 Å
晶胞边长 c length_c	81.300 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	110.01 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.150 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2000
R_work r_work	0.1990
R_free r_free	0.2600

fit	/app/data/saxs_computation/bk/2bkk/2bkk.fit
pddf	/app/data/pr_computation/bk/2bkk/2bkk.pr.out
profile	/app/data/saxs_computation/bk/2bkk/2bkk.dat

;Crystal structure of Aminoglycoside Phosphotransferase APH(3')-IIIa in complex with the inhibitor AR_3a ;

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

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)