SAXSdb — 1kny

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1kny
沉积日期 deposition_date	1995-07-07
结构标题 title	KANAMYCIN NUCLEOTIDYLTRANSFERASE
关键词 keywords	ANTIBIOTIC RESISTANCE, TRANSFERASE, PLASMID; TRANSFERASE
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	24.14 Å
回转半径 Rg (电子) rg_electron	23.16 Å
零角强度 I(0) i0	59882500.00
分子量 molecular_weight	59683.0 kDa
排除体积 excluded_volume	74151 Å³
包络体积 envelope_volume	85949 Å³
水化壳体积 shell_volume	29994 Å³
包络直径 envelope_diameter	71.9 Å
壳层 Rg shell_rg	30.95 Å
包络 Rg envelope_rg	23.00 Å
形状 Rg shape_rg	23.16 Å
总 Rg total_rg	23.94 Å
总原子数 total_atoms	4188
残基数 n_residues	506
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	71.1 Å
Rg (实空间) rg_real	23.94 Å
Rg 误差 (实空间) rg_real_error	0.35 Å
I(0) (实空间) i0_real	5.9880e+07
I(0) 误差 (实空间) i0_real_error	7.5510e+05
Rg (倒空间) rg_reciprocal	23.99 Å
I(0) (倒空间) i0_reciprocal	59880000.0000
解质量估计 total_estimate	0.9116
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	32.2 Å
偏度 Skewness skewness	0.062
峰度 Kurtosis kurtosis	-0.555
角度范围 angular_range	— – 0.3300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13610000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.988

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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	KANAMYCIN NUCLEOTIDYLTRANSFERASE
分子量 formula_weight	28873.6 kDa
EC 编号 ec_number	2.7.7.-
突变 mutation	D80Y
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	4231

MNGPIIMTREERMKIVHEIKERILDKYGDDVKAIGVYGSLGRQTDGPYSDIEMMCVMSTEEAEFSHEWTTGEWKVEVNFYSEEILLDYASQVESDWPLTHGQFFSILPIYDSGGYLEKVYQTAKSVEAQTFHDAICALIVEELFEYAGKWRNIRVQGPTTFLPSLTVQVAMAGAMLIGLHHRICYTTSASVLTEAVKQSDLPSGYDHLCQFVMSGQLSDSEKLLESLENFWNGIQEWTERHGYIVDVSKRIPF

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI 分类编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Entity 2 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	2

Entity 3 non-polymer

描述 description	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
分子量 formula_weight	505.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	KANAMYCIN A
分子量 formula_weight	484.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	43

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1knya1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.16 — Nucleotidyltransferase substrate binding subunit/domain
家族 Family family	a.24.16.1 — Kanamycin nucleotidyltransferase (KNTase), C-terminal domain

结构域编号 domain_id	d1knya2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.218 — Nucleotidyltransferase
超家族 Superfamily superfamily	d.218.1 — Nucleotidyltransferase
家族 Family family	d.218.1.1 — Kanamycin nucleotidyltransferase (KNTase), N-terminal domain

结构域编号 domain_id	d1knyb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.16 — Nucleotidyltransferase substrate binding subunit/domain
家族 Family family	a.24.16.1 — Kanamycin nucleotidyltransferase (KNTase), C-terminal domain

结构域编号 domain_id	d1knyb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.218 — Nucleotidyltransferase
超家族 Superfamily superfamily	d.218.1 — Nucleotidyltransferase
家族 Family family	d.218.1.1 — Kanamycin nucleotidyltransferase (KNTase), N-terminal domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1knyA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	460 — Beta Polymerase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Beta Polymerase, domain 2

结构域编号 domain_id	1knyA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

结构域编号 domain_id	1knyB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	460 — Beta Polymerase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Beta Polymerase, domain 2

结构域编号 domain_id	1knyB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	57.300 Å
晶胞边长 b length_b	102.200 Å
晶胞边长 c length_c	108.800 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	2.500 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.1680
R_free r_free	—

fit	/app/data/saxs_computation/kn/1kny/1kny.fit
pddf	/app/data/pr_computation/kn/1kny/1kny.pr.out
profile	/app/data/saxs_computation/kn/1kny/1kny.dat

KANAMYCIN NUCLEOTIDYLTRANSFERASE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution