3c1l

Crystal structure of an antioxidant defense protein (mlr4105) from mesorhizobium loti maff303099 at 2.00 A resolution

Method: X-RAY DIFFRACTION

▼

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

Putative antioxidant defense protein Mlr4105

Mesorhizobium loti

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	DI(HYDROXYETHYL)ETHER × 16 water × 6	与蛋白数一致
2	蛋白同源多聚体	同源多聚体	蛋白 6	DI(HYDROXYETHYL)ETHER × 9 CHLORIDE ION × 1 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	Q98ES4_RHILO
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 2–188； UniProt 1–187 作者链 B； PDB构建体 2–188； UniProt 1–187 作者链 C； PDB构建体 2–188； UniProt 1–187 作者链 D； PDB构建体 2–188； UniProt 1–187 作者链 E； PDB构建体 2–188； UniProt 1–187 作者链 F； PDB构建体 2–188； UniProt 1–187 作者链 G； PDB构建体 2–188； UniProt 1–187 作者链 H； PDB构建体 2–188； UniProt 1–187 作者链 I； PDB构建体 2–188； UniProt 1–187 作者链 J； PDB构建体 2–188； UniProt 1–187 作者链 K； PDB构建体 2–188； UniProt 1–187 作者链 L； PDB构建体 2–188； UniProt 1–187

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。

▼

2. 结构基本信息 2. Structure Basics

条目编号 entry_id	3c1l
沉积日期 deposition_date	2008-01-23
结构标题 title	Crystal structure of an antioxidant defense protein (mlr4105) from mesorhizobium loti maff303099 at 2.00 A resolution
关键词 keywords	Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, oxidoreductase; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

▼

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。

3c1l__assembly_2__model_1

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

下载该曲线 .dat

3c1l__assembly_2__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

3c1l__assembly_2__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	30.84 Å
Rg（电子密度）	29.95 Å
总 Rg	30.52 Å
原子数	8307
残基数	1042
排除体积	148270 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	`3c1l__assembly_1__model_1`	hexameric （6）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`3c1l__assembly_2__model_1`	hexameric （6）	成功	4.1.3-1-20251215 (887e7ef)	查看下载

▶

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

▶

5. 实体与聚合物信息 Entities & Polymers (4)

实体 1 Entity 1 polymer

描述 description	Putative antioxidant defense protein Mlr4105
分子量 formula_weight	21038.7 kDa
来源方法 src_method	man
拷贝数 entity_count	12

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	17569

GMTGKISALDLASGELSEPTKAYFAKCEEKLGLVPNVLKAYAFDDKKLRAFTDIYNDLMLGESGLSKLDREMIAVAVSSINHCYYCLTAHGAAVRQLSGDPALGEMLVMNFRAADLSPRQTAMLEFAVKLTEEPAKIVEADRAALRKAGFSDRDIWDIASTAAFFNMSNRVAAAIDMRPNDEYHAMAR

来源 Source

来源生物 organism	Mesorhizobium loti
NCBI 分类编号 ncbi_taxonomy_id	266835
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	25

实体 3 Entity 3 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 4 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	731

▼

6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d3c1la_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.152 — AhpD-like
超家族 Superfamily superfamily	a.152.1 — AhpD-like
家族 Family family	a.152.1.3 — Atu0492-like

结构域编号 domain_id	d3c1lb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.152 — AhpD-like
超家族 Superfamily superfamily	a.152.1 — AhpD-like
家族 Family family	a.152.1.3 — Atu0492-like

结构域编号 domain_id	d3c1lc_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.152 — AhpD-like
超家族 Superfamily superfamily	a.152.1 — AhpD-like
家族 Family family	a.152.1.3 — Atu0492-like

结构域编号 domain_id	d3c1ld_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.152 — AhpD-like
超家族 Superfamily superfamily	a.152.1 — AhpD-like
家族 Family family	a.152.1.3 — Atu0492-like

结构域编号 domain_id	d3c1le_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.152 — AhpD-like
超家族 Superfamily superfamily	a.152.1 — AhpD-like
家族 Family family	a.152.1.3 — Atu0492-like

结构域编号 domain_id	d3c1lf_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.152 — AhpD-like
超家族 Superfamily superfamily	a.152.1 — AhpD-like
家族 Family family	a.152.1.3 — Atu0492-like

结构域编号 domain_id	d3c1lg_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.152 — AhpD-like
超家族 Superfamily superfamily	a.152.1 — AhpD-like
家族 Family family	a.152.1.3 — Atu0492-like

结构域编号 domain_id	d3c1lh_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.152 — AhpD-like
超家族 Superfamily superfamily	a.152.1 — AhpD-like
家族 Family family	a.152.1.3 — Atu0492-like

结构域编号 domain_id	d3c1li_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.152 — AhpD-like
超家族 Superfamily superfamily	a.152.1 — AhpD-like
家族 Family family	a.152.1.3 — Atu0492-like

结构域编号 domain_id	d3c1lj_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.152 — AhpD-like
超家族 Superfamily superfamily	a.152.1 — AhpD-like
家族 Family family	a.152.1.3 — Atu0492-like

结构域编号 domain_id	d3c1lk_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.152 — AhpD-like
超家族 Superfamily superfamily	a.152.1 — AhpD-like
家族 Family family	a.152.1.3 — Atu0492-like

结构域编号 domain_id	d3c1ll_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.152 — AhpD-like
超家族 Superfamily superfamily	a.152.1 — AhpD-like
家族 Family family	a.152.1.3 — Atu0492-like

CATH v4.4 (24 domains)

结构域编号 domain_id	3c1lA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	810 — AhpD-like

结构域编号 domain_id	3c1lA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1290 — AhpD-like
同源超家族 H-superfamily homologous superfamily	10 — AhpD-like

结构域编号 domain_id	3c1lB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	810 — AhpD-like

结构域编号 domain_id	3c1lB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1290 — AhpD-like
同源超家族 H-superfamily homologous superfamily	10 — AhpD-like

结构域编号 domain_id	3c1lC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	810 — AhpD-like

结构域编号 domain_id	3c1lC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1290 — AhpD-like
同源超家族 H-superfamily homologous superfamily	10 — AhpD-like

结构域编号 domain_id	3c1lD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	810 — AhpD-like

结构域编号 domain_id	3c1lD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1290 — AhpD-like
同源超家族 H-superfamily homologous superfamily	10 — AhpD-like

结构域编号 domain_id	3c1lE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	810 — AhpD-like

结构域编号 domain_id	3c1lE02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1290 — AhpD-like
同源超家族 H-superfamily homologous superfamily	10 — AhpD-like

结构域编号 domain_id	3c1lF01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	810 — AhpD-like

结构域编号 domain_id	3c1lF02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1290 — AhpD-like
同源超家族 H-superfamily homologous superfamily	10 — AhpD-like

结构域编号 domain_id	3c1lG01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	810 — AhpD-like

结构域编号 domain_id	3c1lG02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1290 — AhpD-like
同源超家族 H-superfamily homologous superfamily	10 — AhpD-like

结构域编号 domain_id	3c1lH01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	810 — AhpD-like

结构域编号 domain_id	3c1lH02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1290 — AhpD-like
同源超家族 H-superfamily homologous superfamily	10 — AhpD-like

结构域编号 domain_id	3c1lI01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	810 — AhpD-like

结构域编号 domain_id	3c1lI02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1290 — AhpD-like
同源超家族 H-superfamily homologous superfamily	10 — AhpD-like

结构域编号 domain_id	3c1lJ01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	810 — AhpD-like

结构域编号 domain_id	3c1lJ02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1290 — AhpD-like
同源超家族 H-superfamily homologous superfamily	10 — AhpD-like

结构域编号 domain_id	3c1lK01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	810 — AhpD-like

结构域编号 domain_id	3c1lK02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1290 — AhpD-like
同源超家族 H-superfamily homologous superfamily	10 — AhpD-like

结构域编号 domain_id	3c1lL01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	810 — AhpD-like

结构域编号 domain_id	3c1lL02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1290 — AhpD-like
同源超家族 H-superfamily homologous superfamily	10 — AhpD-like

▶

晶胞边长 a length_a	65.690 Å
晶胞边长 b length_b	68.060 Å
晶胞边长 c length_c	266.830 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.94 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	29.814 Å
R 因子 r_factor	0.1740
R_work r_work	0.1710
R_free r_free	0.2250

Crystal structure of an antioxidant defense protein (mlr4105) from mesorhizobium loti maff303099 at 2.00 A resolution

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

Putative antioxidant defense protein Mlr4105

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

3c1l__assembly_2__model_1

3c1l__assembly_2__model_1 | I(q)

3c1l__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

5. 实体与聚合物信息 Entities & Polymers (4)

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 non-polymer

实体 4 Entity 4 water

6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. 引用文献 (1)

Crystal structure of an antioxidant defense protein (mlr4105) from mesorhizobium loti maff303099 at 2.00 A resolution

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

Putative antioxidant defense protein Mlr4105

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

3c1l__assembly_2__model_1

3c1l__assembly_2__model_1 | I(q)

3c1l__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

5. 实体与聚合物信息 Entities & Polymers (4)

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 non-polymer

实体 4 Entity 4 water

6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. 引用文献 (1)