1skm

HhaI methyltransferase in complex with DNA containing an abasic south carbocyclic sugar at its target site

Method: X-RAY DIFFRACTION D_max: 72.2 Å Quality: GOOD

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	1skm
沉积日期 deposition_date	2004-03-05
结构标题 title	HhaI methyltransferase in complex with DNA containing an abasic south carbocyclic sugar at its target site
关键词 keywords	PROTEIN-DNA COMPLEX Containing Constrained Abasic Unnatural base, TRANSFERASE-DNA COMPLEX; TRANSFERASE/DNA
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	21.72 Å
回转半径 Rg (电子) rg_electron	20.70 Å
零角强度 I(0) i0	40339500.00
分子量 molecular_weight	44681.0 kDa
排除体积 excluded_volume	53925 Å³
包络体积 envelope_volume	62559 Å³
水化壳体积 shell_volume	24705 Å³
包络直径 envelope_diameter	78.9 Å
壳层 Rg shell_rg	27.99 Å
包络 Rg envelope_rg	21.04 Å
形状 Rg shape_rg	20.68 Å
总 Rg total_rg	21.55 Å
总原子数 total_atoms	3116
残基数 n_residues	351
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	72.2 Å
Rg (实空间) rg_real	21.62 Å
Rg 误差 (实空间) rg_real_error	0.47 Å
I(0) (实空间) i0_real	4.0340e+07
I(0) 误差 (实空间) i0_real_error	4.6190e+05
Rg (倒空间) rg_reciprocal	21.64 Å
I(0) (倒空间) i0_reciprocal	40340000.0000
解质量估计 total_estimate	0.7962
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	26.9 Å
偏度 Skewness skewness	0.249
峰度 Kurtosis kurtosis	-0.290
角度范围 angular_range	— – 0.3650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7913000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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 (5)

Entity 1 polymer

描述 description	5'-D(TPCPCPAPTPGPCPGPCPTPGPAP*C)-3'
分子量 formula_weight	3927.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C
原子数 atom_count	3373

TCCATGCGCTGAC

Entity 2 polymer

描述 description	5'-D(TGPTPCPAPGP(HCX)PGPCPAPTPGP*G)-3'
分子量 formula_weight	3892.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	D

TGTCAGXGCATGG

Entity 3 polymer

描述 description	Modification methylase HhaI
分子量 formula_weight	37042.2 kDa
EC 编号 ec_number	2.1.1.37
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

MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGFPCQAFSISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGQGERIYSTRGIAITLSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYKQFGNSVVINVLQYIAYNIGSSLNFKPY

来源 Source

来源生物 organism	Haemophilus haemolyticus
NCBI 分类编号 ncbi_taxonomy_id	726
宿主生物 host_organism	Escherichia coli

Entity 4 non-polymer

描述 description	S-ADENOSYL-L-HOMOCYSTEINE
分子量 formula_weight	384.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	257

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6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1skma_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.26 — C5 cytosine-specific DNA methylase, DCM

CATH v4.4 (2 domains)

结构域编号 domain_id	1skmA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1skmA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	120 — DNA Methylase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — DNA Methylase, subunit A, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	95.681 Å
晶胞边长 b length_b	95.681 Å
晶胞边长 c length_c	315.683 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	120.00 °
晶胞分子数 Z z_pdb	18

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	24.530 Å
R 因子 r_factor	0.1830
R_work r_work	0.1830
R_free r_free	0.2210

fit	/app/data/saxs_computation/sk/1skm/1skm.fit
pddf	/app/data/pr_computation/sk/1skm/1skm.pr.out
profile	/app/data/saxs_computation/sk/1skm/1skm.dat

HhaI methyltransferase in complex with DNA containing an abasic south carbocyclic sugar at its target site

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

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)