1u8r

Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions

Method: X-RAY DIFFRACTION D_max: 143.8 Å Quality: GOOD

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Iron-dependent repressor ideR

Mycobacterium tuberculosis

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白–DNA 同源多聚体蛋白 × 4 DNA 2 PDB 声明：hexameric（6）与全部聚合物数一致	链 A； UniProt 1–230 链 B； UniProt 1–230 链 C； UniProt 1–230 链 D； UniProt 1–230	未记录	mbtA operator DNA × 1 mbtB operator DNA × 1 CO COBALT (II) ION × 12 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；7% w/v PEG 8000, 0.2 M calcium acetate, 0.1 M imidazole, 0.01 M cobalt chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 2.75 Å R-free 0.265
2	蛋白–DNA 同源多聚体蛋白 × 4 DNA 2 PDB 声明：hexameric（6）与全部聚合物数一致	链 G； UniProt 1–230 链 H； UniProt 1–230 链 I； UniProt 1–230 链 J； UniProt 1–230	未记录	mbtA operator DNA × 1 mbtB operator DNA × 1 CO COBALT (II) ION × 12 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；7% w/v PEG 8000, 0.2 M calcium acetate, 0.1 M imidazole, 0.01 M cobalt chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 2.75 Å R-free 0.265

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 1U8R	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1B1B IRON DEPENDENT REGULATOR 提交 1998-11-19	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–140（140 aa）	未记录	ZN ZINC ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 7.5；pH 7.50	分辨率 2.60 Å R-free 0.360
1FX7 CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS 提交 2000-09-25	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 1–230（230 aa）链 B 1–230（230 aa）	未记录	SO4 SULFATE ION × 11 CO COBALT (II) ION × 6	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；2.0 M lithium sulfate 0.01 M magnesium chloride 0.1 M MES buffer ~0.1 mM 21 bp duplex DNA oligomer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 20K	分辨率 2.00 Å R-free 0.272
1FX7 CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS 提交 2000-09-25	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 C 1–230（230 aa）链 D 1–230（230 aa）	未记录	SO4 SULFATE ION × 6 CO COBALT (II) ION × 7	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；2.0 M lithium sulfate 0.01 M magnesium chloride 0.1 M MES buffer ~0.1 mM 21 bp duplex DNA oligomer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 20K	分辨率 2.00 Å R-free 0.272
1FX7 CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS 提交 2000-09-25	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–230（230 aa）链 B 1–230（230 aa）链 C 1–230（230 aa）链 D 1–230（230 aa）	未记录	SO4 SULFATE ION × 17 CO COBALT (II) ION × 13	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；2.0 M lithium sulfate 0.01 M magnesium chloride 0.1 M MES buffer ~0.1 mM 21 bp duplex DNA oligomer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 20K	分辨率 2.00 Å R-free 0.272
1FX7 CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS 提交 2000-09-25	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 4 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–230（230 aa）链 B 1–230（230 aa）链 C 1–230（230 aa）链 D 1–230（230 aa）	未记录	SO4 SULFATE ION × 17 CO COBALT (II) ION × 13	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；2.0 M lithium sulfate 0.01 M magnesium chloride 0.1 M MES buffer ~0.1 mM 21 bp duplex DNA oligomer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 20K	分辨率 2.00 Å R-free 0.272
1FX7 CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS 提交 2000-09-25	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 5 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–230（230 aa）链 B 1–230（230 aa）链 C 1–230（230 aa）链 D 1–230（230 aa）	未记录	SO4 SULFATE ION × 17 CO COBALT (II) ION × 13	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；2.0 M lithium sulfate 0.01 M magnesium chloride 0.1 M MES buffer ~0.1 mM 21 bp duplex DNA oligomer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 20K	分辨率 2.00 Å R-free 0.272
2ISY Crystal structure of the nickel-activated two-domain iron-dependent regulator (IdeR) 提交 2006-10-18	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 1–140（140 aa）链 B 1–140（140 aa）	非标准单体：是（mmCIF未提供具体位点）非标准单体：是（mmCIF未提供具体位点）	NI NICKEL (II) ION × 4 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.2；298 K；0.6 M Na/K phosphate pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	分辨率 1.96 Å R-free 0.211
2ISZ Crystal structure of a two-domain IdeR-DNA complex crystal form I 提交 2006-10-18	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 同源多聚体；蛋白 × 4 PDB 声明：hexameric	链 A 1–140（140 aa）链 B 1–140（140 aa）链 C 1–140（140 aa）链 D 1–140（140 aa）	未记录	NI NICKEL (II) ION × 12 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；28% PEG 3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	分辨率 2.40 Å R-free 0.239
2IT0 Crystal structure of a two-domain IdeR-DNA complex crystal form II 提交 2006-10-18	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 同源多聚体；蛋白 × 4 PDB 声明：hexameric	链 A 1–140（140 aa）链 B 1–140（140 aa）链 C 1–140（140 aa）链 D 1–140（140 aa）	未记录	NI NICKEL (II) ION × 12 ACT ACETATE ION × 10	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；26% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris HCl pH 8.5, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K	分辨率 2.60 Å R-free 0.273

共 5 个其他 PDB 条目、9 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	IDER_MYCTU
Isoform	—
PDB实体	3
链与序列区间	作者链 A； PDB构建体 1–230； UniProt 1–230 作者链 B； PDB构建体 1–230； UniProt 1–230 作者链 C； PDB构建体 1–230； UniProt 1–230 作者链 D； PDB构建体 1–230； UniProt 1–230 作者链 G； PDB构建体 1–230； UniProt 1–230 作者链 H； PDB构建体 1–230； UniProt 1–230 作者链 I； PDB构建体 1–230； UniProt 1–230 作者链 J； PDB构建体 1–230； UniProt 1–230

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

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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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	1u8r
沉积日期 deposition_date	2004-08-06
结构标题 title	Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions
关键词 keywords	;IdeR, iron-dependent regulator, iron acquisition, siderophores, Mycobacterium tuberculosis, metal-binding protein, Transcription-DNA COMPLEX ;; metal-binding protein,Transcription/DNA
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	45.67 Å
回转半径 Rg (电子) rg_electron	45.82 Å
零角强度 I(0) i0	1058160000.00
分子量 molecular_weight	237470.0 kDa
排除体积 excluded_volume	284390 Å³
包络体积 envelope_volume	429810 Å³
水化壳体积 shell_volume	78294 Å³
包络直径 envelope_diameter	147.6 Å
壳层 Rg shell_rg	51.22 Å
包络 Rg envelope_rg	43.79 Å
形状 Rg shape_rg	45.86 Å
总 Rg total_rg	45.90 Å
总原子数 total_atoms	16430
残基数 n_residues	1902
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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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	143.8 Å
Rg (实空间) rg_real	45.46 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	1.0580e+09
I(0) 误差 (实空间) i0_real_error	1.7970e+07
Rg (倒空间) rg_reciprocal	45.67 Å
I(0) (倒空间) i0_reciprocal	1058000000.0000
解质量估计 total_estimate	0.8794
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	57.5 Å
偏度 Skewness skewness	0.159
峰度 Kurtosis kurtosis	-0.382
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	42640000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.717

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5. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (6)

实体 1 Entity 1 polymer

描述 description	mbtA operator DNA
分子量 formula_weight	10112.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polydeoxyribonucleotide
链编号 strand_id	E,K
原子数 atom_count	16481

CCCTGTTAGCACAGGCTGCCCTAATTTTAGTGG

实体 2 Entity 2 polymer

描述 description	mbtB operator DNA
分子量 formula_weight	10188.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polydeoxyribonucleotide
链编号 strand_id	F,L

CACTAAAATTAGGGCAGCCTGTGCTAACAGGGC

实体 3 Entity 3 polymer

描述 description	Iron-dependent repressor ideR
分子量 formula_weight	25281.8 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,G,H,I,J

MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLDELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQGDIDLITRLKDAGVVPNARVTVETTPGGGVTIVIPGHENVTLPHEMAHAVKVEKV

来源 Source

来源生物 organism	Mycobacterium tuberculosis
NCBI 分类编号 ncbi_taxonomy_id	1773
宿主生物 host_organism	Escherichia coli

实体 4 Entity 4 non-polymer

描述 description	COBALT (II) ION
分子量 formula_weight	58.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	24

实体 5 Entity 5 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

实体 6 Entity 6 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	51

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7. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

结构域编号 domain_id	d1u8ra1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.24 — Iron-dependent repressor protein

结构域编号 domain_id	d1u8ra2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
超家族 Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
家族 Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

结构域编号 domain_id	d1u8ra3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
家族 Family family	b.34.1.2 — FeoA-like

结构域编号 domain_id	d1u8rb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.24 — Iron-dependent repressor protein

结构域编号 domain_id	d1u8rb2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
超家族 Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
家族 Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

结构域编号 domain_id	d1u8rb3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
家族 Family family	b.34.1.2 — FeoA-like

结构域编号 domain_id	d1u8rc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.24 — Iron-dependent repressor protein

结构域编号 domain_id	d1u8rc2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
超家族 Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
家族 Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

结构域编号 domain_id	d1u8rc3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
家族 Family family	b.34.1.2 — FeoA-like

结构域编号 domain_id	d1u8rd1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.24 — Iron-dependent repressor protein

结构域编号 domain_id	d1u8rd2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
超家族 Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
家族 Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

结构域编号 domain_id	d1u8rd3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
家族 Family family	b.34.1.2 — FeoA-like

结构域编号 domain_id	d1u8rg1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.24 — Iron-dependent repressor protein

结构域编号 domain_id	d1u8rg2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
超家族 Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
家族 Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

结构域编号 domain_id	d1u8rg3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
家族 Family family	b.34.1.2 — FeoA-like

结构域编号 domain_id	d1u8rh1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.24 — Iron-dependent repressor protein

结构域编号 domain_id	d1u8rh2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
超家族 Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
家族 Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

结构域编号 domain_id	d1u8rh3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
家族 Family family	b.34.1.2 — FeoA-like

结构域编号 domain_id	d1u8ri1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.24 — Iron-dependent repressor protein

结构域编号 domain_id	d1u8ri2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
超家族 Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
家族 Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

结构域编号 domain_id	d1u8ri3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
家族 Family family	b.34.1.2 — FeoA-like

结构域编号 domain_id	d1u8rj1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.24 — Iron-dependent repressor protein

结构域编号 domain_id	d1u8rj2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
超家族 Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
家族 Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

结构域编号 domain_id	d1u8rj3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
家族 Family family	b.34.1.2 — FeoA-like

CATH v4.4 (24 domains)

结构域编号 domain_id	1u8rA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1u8rA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	60 — Diphtheria Toxin Repressor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

结构域编号 domain_id	1u8rA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

结构域编号 domain_id	1u8rB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1u8rB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	60 — Diphtheria Toxin Repressor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

结构域编号 domain_id	1u8rB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

结构域编号 domain_id	1u8rC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1u8rC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	60 — Diphtheria Toxin Repressor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

结构域编号 domain_id	1u8rC03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

结构域编号 domain_id	1u8rD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1u8rD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	60 — Diphtheria Toxin Repressor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

结构域编号 domain_id	1u8rD03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

结构域编号 domain_id	1u8rG01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1u8rG02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	60 — Diphtheria Toxin Repressor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

结构域编号 domain_id	1u8rG03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

结构域编号 domain_id	1u8rH01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1u8rH02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	60 — Diphtheria Toxin Repressor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

结构域编号 domain_id	1u8rH03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

结构域编号 domain_id	1u8rI01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1u8rI02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	60 — Diphtheria Toxin Repressor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

结构域编号 domain_id	1u8rI03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

结构域编号 domain_id	1u8rJ01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1u8rJ02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	60 — Diphtheria Toxin Repressor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

结构域编号 domain_id	1u8rJ03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

▶

8. 引用文献 (1)

▶

晶胞边长 a length_a	107.959 Å
晶胞边长 b length_b	107.959 Å
晶胞边长 c length_c	215.124 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 31
空间群编号 int_tables_number	144
晶系 crystal_system	—

分辨率 resolution	2.750 Å
最低分辨率 resolution_low	46.750 Å
R 因子 r_factor	0.2320
R_work r_work	0.2300
R_free r_free	0.2650

Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions

1. 蛋白身份与相关结构 Protein Identity & Related Structures

Iron-dependent repressor ideR

当前结构中的状态

数据库中的同蛋白其他状态

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

2. 结构基本信息 2. Structure Basics

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

5. 晶体学与实验 5. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

6. 实体与聚合物信息 Entities & Polymers (6)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 polymer

聚合物 Polymer

实体 3 Entity 3 polymer

聚合物 Polymer

来源 Source

实体 4 Entity 4 non-polymer

实体 5 Entity 5 non-polymer

实体 6 Entity 6 water

7. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/u8/1u8r/1u8r.fit
pddf	/app/data/pr_computation/u8/1u8r/1u8r.pr.out
profile	/app/data/saxs_computation/u8/1u8r/1u8r.dat