8q56

PglX methyltransferase of Salmonella BREX phage defence system (aka BrxX) bound to inhibitor Ocr

Method: X-RAY DIFFRACTION D_max: 129.3 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	8q56
沉积日期 deposition_date	2023-08-08
结构标题 title	PglX methyltransferase of Salmonella BREX phage defence system (aka BrxX) bound to inhibitor Ocr
关键词 keywords	Methyltransferase, Phage defense, DNA binding, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	40.32 Å
回转半径 Rg (电子) rg_electron	39.82 Å
零角强度 I(0) i0	345784000.00
分子量 molecular_weight	152770.0 kDa
排除体积 excluded_volume	191420 Å³
包络体积 envelope_volume	253420 Å³
水化壳体积 shell_volume	53159 Å³
包络直径 envelope_diameter	137.3 Å
壳层 Rg shell_rg	45.02 Å
包络 Rg envelope_rg	39.59 Å
形状 Rg shape_rg	39.81 Å
总 Rg total_rg	40.14 Å
总原子数 total_atoms	10796
残基数 n_residues	1318
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	129.3 Å
Rg (实空间) rg_real	40.40 Å
Rg 误差 (实空间) rg_real_error	0.99 Å
I(0) (实空间) i0_real	3.4580e+08
I(0) 误差 (实空间) i0_real_error	5.6310e+06
Rg (倒空间) rg_reciprocal	40.32 Å
I(0) (倒空间) i0_reciprocal	345800000.0000
解质量估计 total_estimate	0.8660
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	39.8 Å
偏度 Skewness skewness	0.347
峰度 Kurtosis kurtosis	-0.632
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	78560000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.651

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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	site-specific DNA-methyltransferase (adenine-specific)
分子量 formula_weight	141507.4 kDa
EC 编号 ec_number	2.1.1.72
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	10798

MNTNNIKKYAPQARNQFRDAVIQKLTTLGISADKKGNLQIADAELVGETMRYGQFDYPKSTLTRRDRLVKRAREQGFDVLVEHCAYTWFNRLCAIRYMEIHGYLDHGFHMLSHPDNPTGFEVLDHVPEVAEALLPEKKAQLVEMKLSGNQDEAIYRELLLAQCHALHRAMPFLFEAVDDEAELLLPDNLTRTDSILRGLVDGIPEEDWQEVEVIGWLYQFYISEKKDAVIGKVVKSEDIPAATQLFTPNWIVQYLVQNSVGRQWLQTYPDSPLKGKMDYYIEPAEQTPEVQAQLAAITPASIEPESIKVLDPACGSGHILIEVYNVLKNIYEERGYRARDIPQLILENNIFGLDIDDRAAQLSGFALLMMARQDDRRIFTRDVRLNIVSLQESLHLDIAKLWQQLNFHQQNQTGSMGDMFAENTALAHTDSAEYQLLMRTLKRFVNAKTLGSLIQVPQEEEAELKAFLEALYRMEQEGDFQQKAAAKAFIPYIQQAWILAQRYDAVVANPPYMGGKGMNSELKEFAKNNFPDSKADLFAMFMQNAFSLLKENGFNAQVNMQSWMFLSSYEALRNWLLDNKTFITMAHLGARAFGQISGEVVQTTAWVIKNQHSERYQPVFFRLIDGREEVKKSDLLLRKNIFDKFTQHDFKNIPGMPIAYWIDLPSLLSFRHHKKLGEKIALKAGMSTGDNIKFQRYWYEVSIKKTLITNKESNTKIDIHNIKWFPCSSGGEYRKWYGNNEIVVNWENNGYEIRNFKFENGKTRSAVRNDEYYFREGITWSKISQGNFCVRYRPKGFVFDDTGRCGFSNNKNELLYAAGLMCTPVVNHYLSILAPTLSFTSGELASVPYPEIEDEIIELVTNAIEIAKNDWDSQEQSWDYVCSPLLEHNSTQLLRNIYKQKINTNIKLVETLLLIENTINNIFIDKLQLDKTIIKAVLQSEITLLCNPNYRYKNIQDHTDLTNKYYTDITIDILSYIIGCMMGRYSLDREGLVYAHEGNKGFAELVAEDAYKTFPADNDGILPLMDDEWFDDDVTSRVKEFVRTVWGEEHLQENLEFIAESLCLYAIKPKKGESALDTIRRYLSTQFWKDHMKMYKKRPIYWLFSSGKEKAFECLVYLHRYNDATLARMRTEYVVPLLARYQANIDRLNEQVDGASGGEATRLKRERDSLSKKFNELRSFDDRLRHYADMRISIDLDDGVKVNYGKFGDLLADVKAITGNAPEII

来源 Source

来源生物 organism	Salmonella enterica subsp. enterica serovar Typhimurium str. D23580
NCBI 分类编号 ncbi_taxonomy_id	568708
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Protein Ocr
分子量 formula_weight	13819.0 kDa
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	B

MAMSNMTYNNVFDHAYEMLKENIRYDDIRDTDDLHDAIHMAADNAVPHYYADIFSVMASEGIDLEFEDSGLMPDTKDVIRILQARIYEQLTIDLWEDAEDLLNEYLEEVEEYEEDEE

来源 Source

来源生物 organism	Escherichia phage T7
NCBI 分类编号 ncbi_taxonomy_id	10760
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

描述 description	S-ADENOSYLMETHIONINE
分子量 formula_weight	398.4 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	2

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7. 引用文献 (1)

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晶胞边长 a length_a	238.458 Å
晶胞边长 b length_b	60.786 Å
晶胞边长 c length_c	146.637 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	114.89 °
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	monoclinic

分辨率 resolution	3.500 Å
最低分辨率 resolution_low	59.610 Å
R 因子 r_factor	0.2518
R_work r_work	0.2462
R_free r_free	0.2917

fit	/app/data/saxs_computation/q5/8q56/8q56.fit
pddf	/app/data/pr_computation/q5/8q56/8q56.pr.out
profile	/app/data/saxs_computation/q5/8q56/8q56.dat

PglX methyltransferase of Salmonella BREX phage defence system (aka BrxX) bound to inhibitor Ocr

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 (4)

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 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)