1nmo

Structural genomics, protein ybgI, unknown function

Method: X-RAY DIFFRACTION

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

Hypothetical protein ybgI

Escherichia coli, Escherichia coli O157:H7

当前结构中的状态

Assembly	物理组成	蛋白状态	分子拷贝数	共同组分	数据核对
1	蛋白同源多聚体	同源多聚体	蛋白 6	FE (III) ION × 12 water × 6	与蛋白数一致
2	蛋白同源多聚体	同源多聚体	蛋白 6	FE (III) ION × 12 water × 6	与蛋白数一致
3	蛋白同源多聚体	同源多聚体	蛋白 6	FE (III) ION × 12 water × 6	与蛋白数一致
4	蛋白同源多聚体	同源多聚体	蛋白 6	FE (III) ION × 12 water × 6	与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据

UniProt名称	YBGI_ECOLI
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–247； UniProt 1–247 作者链 B； PDB构建体 1–247； UniProt 1–247 作者链 C； PDB构建体 1–247； UniProt 1–247 作者链 D； PDB构建体 1–247； UniProt 1–247 作者链 E； PDB构建体 1–247； UniProt 1–247 作者链 F； PDB构建体 1–247； UniProt 1–247

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。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	1nmo
沉积日期 deposition_date	2003-01-10
结构标题 title	Structural genomics, protein ybgI, unknown function
关键词 keywords	ybgI, hypothetical protein, toroidal structure, Structure 2 Function Project, S2F, Structural Genomics, unknown function; structural genomics, unknown function
实验方法 method	X-RAY DIFFRACTION

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3. Official assembly/model 理论 SAXS Official SAXS Profiles

页面只读取最新 assembly 计算结果。每一条曲线都对应明确的 PDB、official biological assembly 和 coordinate model。

1nmo__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

1nmo__assembly_2__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

1nmo__assembly_2__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	37.25 Å
Rg（电子密度）	36.36 Å
总 Rg	37.10 Å
原子数	11394
残基数	1458
排除体积	202300 Å³
最大 q	0.500 Å⁻¹

Assembly	Model	结构单元	聚集说明	状态	CRYSOL	操作
1	1	`1nmo__assembly_1__model_1`	hexameric （6）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`1nmo__assembly_2__model_1`	hexameric （6）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
3	1	`1nmo__assembly_3__model_1`	hexameric （6）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
4	1	`1nmo__assembly_4__model_1`	hexameric （6）	成功	4.1.3-1-20251215 (887e7ef)	查看下载

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

描述 description	Hypothetical protein ybgI
分子量 formula_weight	27107.0 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	12031

MKNTELEQLINEKLNSAAISDYAPNGLQVEGKETVQKIVTGVTASQALLDEAVRLGADAVIVHHGYFWKGESPVIRGMKRNRLKTLLANDINLYGWHLPLDAHPELGNNAQLAALLGITVMGEIEPLVPWGELTMPVPGLELASWIEARLGRKPLWCGDTGPEVVQRVAWCTGGGQSFIDSAARFGVDAFITGEVSEQTIHSAREQGLHFYAAGHHATERGGIRALSEWLNENTDLDVTFIDIPNPA

来源 Source

来源生物 organism	Escherichia coli, Escherichia coli O157:H7
通用名 common_name	,
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

实体 3 Entity 3 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	637

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1nmoa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
超家族 Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
家族 Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	d1nmob_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
超家族 Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
家族 Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	d1nmoc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
超家族 Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
家族 Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	d1nmod_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
超家族 Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
家族 Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	d1nmoe_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
超家族 Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
家族 Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	d1nmof_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
超家族 Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
家族 Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

CATH v4.4 (12 domains)

结构域编号 domain_id	1nmoA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmoA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmoB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmoB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmoC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmoC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmoD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmoD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmoE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmoE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmoF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmoF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

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晶胞边长 a length_a	154.660 Å
晶胞边长 b length_b	154.660 Å
晶胞边长 c length_c	57.520 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	P 3
空间群编号 int_tables_number	143
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	19.600 Å
R 因子 r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2590

Structural genomics, protein ybgI, unknown function

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

Hypothetical protein ybgI

当前结构中的状态

数据库中的同蛋白其他状态

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

1nmo__assembly_2__model_1

1nmo__assembly_2__model_1 | I(q)

1nmo__assembly_2__model_1 | P(r) · Pending

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. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

实体 3 Entity 3 water

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

Structural genomics, protein ybgI, unknown function

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

Hypothetical protein ybgI

当前结构中的状态

数据库中的同蛋白其他状态

单体

同源二聚体

同源四聚体

其他同源多聚体

异源或核酸复合物

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

1nmo__assembly_2__model_1

1nmo__assembly_2__model_1 | I(q)

1nmo__assembly_2__model_1 | P(r) · Pending

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. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

实体 3 Entity 3 water

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)