SAXSdb — 1mj2

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1mj2
沉积日期 deposition_date	1998-01-27
结构标题 title	METHIONINE REPRESSOR MUTANT (Q44K) PLUS COREPRESSOR (S-ADENOSYL METHIONINE) COMPLEXED TO A CONSENSUS OPERATOR SEQUENCE
关键词 keywords	;TRANSCRIPTION REGULATION, METJ, METHIONINE REPRESSOR, SHEET-HELIX-HELIX, S-ADENOSYL METHIONINE, DNA, COMPLEX (TRANSCRIPTION REGULATION-DNA), TRANSCRIPTION-DNA COMPLEX ;; TRANSCRIPTION/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	25.83 Å
回转半径 Rg (电子) rg_electron	25.06 Å
零角强度 I(0) i0	79956200.00
分子量 molecular_weight	61300.0 kDa
排除体积 excluded_volume	73048 Å³
包络体积 envelope_volume	89841 Å³
水化壳体积 shell_volume	29766 Å³
包络直径 envelope_diameter	81.8 Å
壳层 Rg shell_rg	32.58 Å
包络 Rg envelope_rg	25.07 Å
形状 Rg shape_rg	25.06 Å
总 Rg total_rg	25.80 Å
总原子数 total_atoms	4261
残基数 n_residues	453
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	79.3 Å
Rg (实空间) rg_real	25.75 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	7.9960e+07
I(0) 误差 (实空间) i0_real_error	1.1350e+06
Rg (倒空间) rg_reciprocal	25.78 Å
I(0) (倒空间) i0_reciprocal	79960000.0000
解质量估计 total_estimate	0.9103
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	29.9 Å
偏度 Skewness skewness	0.218
峰度 Kurtosis kurtosis	-0.507
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8198000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.957

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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	;DNA (5'-D(TPTPAPGPAPCPGPTPCPTPAPGPAPCPGPTPCPTP*A)-3') ;
分子量 formula_weight	5819.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	F,G
原子数 atom_count	4481

TTAGACGTCTAGACGTCTA

Entity 2 polymer

描述 description	PROTEIN (METHIONINE REPRESSOR)
分子量 formula_weight	12028.6 kDa
突变 mutation	Q44K
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D

AEWSGEYISPYAEHGKKSEQVKKITVSIPLKVLKILTDERTRRKVNNLRHATNSELLCEAFLHAFTGQPLPDDADLRKERSDEIPEAAKEIMREMGINPETWEY

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

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	4

Entity 4 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 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	220

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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	d1mj2a_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.43 — Ribbon-helix-helix
超家族 Superfamily superfamily	a.43.1 — Ribbon-helix-helix
家族 Family family	a.43.1.5 — Met repressor, MetJ (MetR)

结构域编号 domain_id	d1mj2b_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.43 — Ribbon-helix-helix
超家族 Superfamily superfamily	a.43.1 — Ribbon-helix-helix
家族 Family family	a.43.1.5 — Met repressor, MetJ (MetR)

结构域编号 domain_id	d1mj2c_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.43 — Ribbon-helix-helix
超家族 Superfamily superfamily	a.43.1 — Ribbon-helix-helix
家族 Family family	a.43.1.5 — Met repressor, MetJ (MetR)

结构域编号 domain_id	d1mj2d_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.43 — Ribbon-helix-helix
超家族 Superfamily superfamily	a.43.1 — Ribbon-helix-helix
家族 Family family	a.43.1.5 — Met repressor, MetJ (MetR)

CATH v4.4 (4 domains)

结构域编号 domain_id	1mj2A00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	140 — MET Apo-Repressor, subunit A
同源超家族 H-superfamily homologous superfamily	10 — MET Apo-Repressor, subunit A

结构域编号 domain_id	1mj2B00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	140 — MET Apo-Repressor, subunit A
同源超家族 H-superfamily homologous superfamily	10 — MET Apo-Repressor, subunit A

结构域编号 domain_id	1mj2C00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	140 — MET Apo-Repressor, subunit A
同源超家族 H-superfamily homologous superfamily	10 — MET Apo-Repressor, subunit A

结构域编号 domain_id	1mj2D00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	140 — MET Apo-Repressor, subunit A
同源超家族 H-superfamily homologous superfamily	10 — MET Apo-Repressor, subunit A

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7. 引用文献 (1)

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晶胞边长 a length_a	117.180 Å
晶胞边长 b length_b	117.180 Å
晶胞边长 c length_c	90.090 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	24

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	33.800 Å
R 因子 r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2600

fit	/app/data/saxs_computation/mj/1mj2/1mj2.fit
pddf	/app/data/pr_computation/mj/1mj2/1mj2.pr.out
profile	/app/data/saxs_computation/mj/1mj2/1mj2.dat

METHIONINE REPRESSOR MUTANT (Q44K) PLUS COREPRESSOR (S-ADENOSYL METHIONINE) COMPLEXED TO A CONSENSUS OPERATOR SEQUENCE

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

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 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)