1s4d

Crystal Structure Analysis of the S-adenosyl-L-methionine dependent uroporphyrinogen-III C-methyltransferase SUMT

Method: X-RAY DIFFRACTION

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

Uroporphyrin-III C-methyltransferase

Pseudomonas denitrificans

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 2	S-ADENOSYL-L-HOMOCYSTEINE × 2 GLYCEROL × 4 water × 2	与蛋白数一致
2	蛋白同源多聚体	同源多聚体	蛋白 2	S-ADENOSYL-L-HOMOCYSTEINE × 2 GLYCEROL × 5 water × 2	与蛋白数一致
3	蛋白同源多聚体	同源多聚体	蛋白 2	S-ADENOSYL-L-HOMOCYSTEINE × 2 GLYCEROL × 5 water × 2	与蛋白数一致
4	蛋白同源多聚体	同源多聚体	蛋白 2	S-ADENOSYL-L-HOMOCYSTEINE × 2 GLYCEROL × 4 water × 2	与蛋白数一致
5	蛋白同源多聚体	同源多聚体	蛋白 2	S-ADENOSYL-L-HOMOCYSTEINE × 2 GLYCEROL × 5 water × 2	与蛋白数一致
6	蛋白同源多聚体	同源多聚体	蛋白 2	S-ADENOSYL-L-HOMOCYSTEINE × 2 GLYCEROL × 3 water × 2	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	SUMT_PSEDE
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–280； UniProt 1–280 作者链 B； PDB构建体 1–280； UniProt 1–280 作者链 D； PDB构建体 1–280； UniProt 1–280 作者链 E； PDB构建体 1–280； UniProt 1–280 作者链 F； PDB构建体 1–280； UniProt 1–280 作者链 G； PDB构建体 1–280； UniProt 1–280 作者链 H； PDB构建体 1–280； UniProt 1–280 作者链 I； PDB构建体 1–280； UniProt 1–280 作者链 J； PDB构建体 1–280； UniProt 1–280 作者链 K； PDB构建体 1–280； UniProt 1–280 作者链 L； PDB构建体 1–280； UniProt 1–280 作者链 M； PDB构建体 1–280； UniProt 1–280

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	1s4d
沉积日期 deposition_date	2004-01-16
结构标题 title	Crystal Structure Analysis of the S-adenosyl-L-methionine dependent uroporphyrinogen-III C-methyltransferase SUMT
关键词 keywords	tetrapyrrole biosynthesis, cobalamin, SAM, SAH, uroporphyrinogen-III methyltransferase, Transferase; TRANSFERASE
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。

1s4d__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

1s4d__assembly_3__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

1s4d__assembly_3__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	23.10 Å
Rg（电子密度）	21.71 Å
总 Rg	22.62 Å
原子数	3811
残基数	512
排除体积	67956 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	`1s4d__assembly_1__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`1s4d__assembly_2__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
3	1	`1s4d__assembly_3__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
4	1	`1s4d__assembly_4__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
5	1	`1s4d__assembly_5__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
6	1	`1s4d__assembly_6__model_1`	dimeric （2）	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 (4)

实体 1 Entity 1 polymer

描述 description	Uroporphyrin-III C-methyltransferase
分子量 formula_weight	29286.8 kDa
EC 编号 ec_number	2.1.1.107
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,D,E,F,G,H,I,J,K,L,M
原子数 atom_count	23427

MIDDLFAGLPALEKGSVWLVGAGPGDPGLLTLHAANALRQADVIVHDALVNEDCLKLARPGAVLEFAGKRGGKPSPKQRDISLRLVELARAGNRVLRLKGGDPFVFGRGGEEALTLVEHQVPFRIVPGITAGIGGLAYAGIPVTHREVNHAVTFLTGHDSSGLVPDRINWQGIASGSPVIVMYMAMKHIGAITANLIAGGRSPDEPVAFVCNAATPQQAVLETTLARAEADVAAAGLEPPAIVVVGEVVRLRAALDWIGALDGRKLAADPFANRILRNPA

来源 Source

来源生物 organism	Pseudomonas denitrificans
NCBI 分类编号 ncbi_taxonomy_id	43306
宿主生物 host_organism	Escherichia coli BL21(DE3)

实体 2 Entity 2 non-polymer

描述 description	S-ADENOSYL-L-HOMOCYSTEINE
分子量 formula_weight	384.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

实体 3 Entity 3 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	26

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	523

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6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1s4da_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1s4db_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1s4dd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1s4de_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1s4df_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1s4dg_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1s4dh_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1s4di_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1s4dj_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1s4dk_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1s4dl_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1s4dm_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

CATH v4.4 (24 domains)

结构域编号 domain_id	1s4dA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1s4dA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

结构域编号 domain_id	1s4dB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1s4dB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

结构域编号 domain_id	1s4dD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1s4dD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

结构域编号 domain_id	1s4dE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1s4dE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

结构域编号 domain_id	1s4dF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1s4dF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

结构域编号 domain_id	1s4dG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1s4dG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

结构域编号 domain_id	1s4dH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1s4dH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

结构域编号 domain_id	1s4dI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1s4dI02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

结构域编号 domain_id	1s4dJ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1s4dJ02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

结构域编号 domain_id	1s4dK01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1s4dK02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

结构域编号 domain_id	1s4dL01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1s4dL02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

结构域编号 domain_id	1s4dM01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1s4dM02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

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晶胞边长 a length_a	218.097 Å
晶胞边长 b length_b	218.097 Å
晶胞边长 c length_c	190.341 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	90.00 °
晶胞分子数 Z z_pdb	96

空间群 space_group	I 4
空间群编号 int_tables_number	79
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	19.840 Å
R 因子 r_factor	0.2153
R_work r_work	0.2129
R_free r_free	0.2603

Crystal Structure Analysis of the S-adenosyl-L-methionine dependent uroporphyrinogen-III C-methyltransferase SUMT

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

Uroporphyrin-III C-methyltransferase

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

1s4d__assembly_3__model_1

1s4d__assembly_3__model_1 | I(q)

1s4d__assembly_3__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 (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 Analysis of the S-adenosyl-L-methionine dependent uroporphyrinogen-III C-methyltransferase SUMT

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

Uroporphyrin-III C-methyltransferase

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

1s4d__assembly_3__model_1

1s4d__assembly_3__model_1 | I(q)

1s4d__assembly_3__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 (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)