3iei

Crystal structure of human leucine carboxylmethyltransferase-1 in complex with S-adenosyl homocysteine

Method: X-RAY DIFFRACTION D_max: 151.6 Å Quality: GOOD

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

Leucine carboxyl methyltransferase 1

Homo sapiens

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	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 A； UniProt 1–334	突变：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 1.90 Å R-free 0.232
2	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 B； UniProt 1–334	突变：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 1.90 Å R-free 0.232
3	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 C； UniProt 1–334	突变：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 1.90 Å R-free 0.232
4	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 D； UniProt 1–334	突变：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 1.90 Å R-free 0.232
5	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 E； UniProt 1–334	突变：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 1.90 Å R-free 0.232
6	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 F； UniProt 1–334	突变：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 1.90 Å R-free 0.232
7	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 G； UniProt 1–334	突变：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 1.90 Å R-free 0.232
8	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 H； UniProt 1–334	突变：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 1.90 Å R-free 0.232

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 3IEI	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
3O7W The Crystal Structure of Human Leucine Carboxyl Methyltransferase 1 提交 2010-08-01	构建体不同突变/修饰不同配体/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 23–334（312 aa）片段：UNP residues 23-334 with deletion of residues 233-258	未记录	GOL GLYCEROL × 1 SAM S-ADENOSYLMETHIONINE × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.05 M Ammonium Sulfate, 0.05M Bis Tris (pH6.5), 30% Pentaerythritol Ethoxylate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	分辨率 2.00 Å R-free 0.265
3P71 Crystal structure of the complex of LCMT-1 and PP2A 提交 2010-10-11	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 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 T 1–334（334 aa）	突变：C19M, A21E, D22N, P115S	PEG DI(HYDROXYETHYL)ETHER × 1 AN6 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；PROTEIN COMPLEX (~5 MG/ML), 100MM TRIS-HCL, 22-26% V/V PEG 4000, 200 MM SODIUM ACETATE, 5 MM DTT, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K	分辨率 2.70 Å R-free 0.249

共 2 个其他 PDB 条目、2 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	LCMT1_HUMAN
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–334； UniProt 1–334 作者链 B； PDB构建体 1–334； UniProt 1–334 作者链 C； PDB构建体 1–334； UniProt 1–334 作者链 D； PDB构建体 1–334； UniProt 1–334 作者链 E； PDB构建体 1–334； UniProt 1–334 作者链 F； PDB构建体 1–334； UniProt 1–334 作者链 G； PDB构建体 1–334； UniProt 1–334 作者链 H； PDB构建体 1–334； UniProt 1–334

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	3iei
沉积日期 deposition_date	2009-07-22
结构标题 title	Crystal structure of human leucine carboxylmethyltransferase-1 in complex with S-adenosyl homocysteine
关键词 keywords	LCMT-1, Methyltransferase, S-adenosyl-L-methionine, Transferase; TRANSFERASE
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	46.66 Å
回转半径 Rg (电子) rg_electron	46.02 Å
零角强度 I(0) i0	1265190000.00
分子量 molecular_weight	290990.0 kDa
排除体积 excluded_volume	362820 Å³
包络体积 envelope_volume	497060 Å³
水化壳体积 shell_volume	88861 Å³
包络直径 envelope_diameter	159.9 Å
壳层 Rg shell_rg	52.04 Å
包络 Rg envelope_rg	44.85 Å
形状 Rg shape_rg	46.00 Å
总 Rg total_rg	46.29 Å
总原子数 total_atoms	20344
残基数 n_residues	2480
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	151.6 Å
Rg (实空间) rg_real	46.47 Å
Rg 误差 (实空间) rg_real_error	1.05 Å
I(0) (实空间) i0_real	1.2650e+09
I(0) 误差 (实空间) i0_real_error	2.2400e+07
Rg (倒空间) rg_reciprocal	46.66 Å
I(0) (倒空间) i0_reciprocal	1265000000.0000
解质量估计 total_estimate	0.8567
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	62.4 Å
偏度 Skewness skewness	0.240
峰度 Kurtosis kurtosis	-0.227
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	144500000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.800

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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 (5)

实体 1 Entity 1 polymer

描述 description	Leucine carboxyl methyltransferase 1
分子量 formula_weight	38504.2 kDa
EC 编号 ec_number	2.1.1.-
突变 mutation	C19M, A21E, D22N, P115S
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,E,F,G,H
原子数 atom_count	22201

MATRQRESSITSCCSTSSMDENDEGVRGTCEDASLCKRFAVSIGYWHDPYIQHFVRLSKERKAPEINRGYFARVHGVSQLIKAFLRKTECHCQIVNLGAGMDTTFWRLKDEDLLSSKYFEVDFPMIVTRKLHSIKCKPPLSSPILELHSEDTLQMDGHILDSKRYAVIGADLRDLSELEEKLKKCNMNTQLPTLLIAECVLVYMTPEQSANLLKWAANSFERAMFINYEQVNMGDRFGQIMIENLRRRQCDLAGVETCKSLESQKERLLSNGWETASAVDMMELYNRLPRAEVSRIESLEFLDEMELLEQLMRHYCLCWATKGGNELGLKEITY

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

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	8

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	8

实体 4 Entity 4 non-polymer

描述 description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
分子量 formula_weight	195.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 5 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	1851

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7. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d3ieia_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.0 — automated matches

结构域编号 domain_id	d3ieib_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.0 — automated matches

结构域编号 domain_id	d3ieic_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.0 — automated matches

结构域编号 domain_id	d3ieid_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.0 — automated matches

结构域编号 domain_id	d3ieie_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.0 — automated matches

结构域编号 domain_id	d3ieif_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.0 — automated matches

结构域编号 domain_id	d3ieig_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.0 — automated matches

结构域编号 domain_id	d3ieih_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.0 — automated matches

CATH v4.4 (8 domains)

结构域编号 domain_id	3ieiA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	3ieiB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	3ieiC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	3ieiD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	3ieiE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	3ieiF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	3ieiG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	3ieiH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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8. 引用文献 (1)

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晶胞边长 a length_a	106.036 Å
晶胞边长 b length_b	81.127 Å
晶胞边长 c length_c	82.816 Å
晶胞夹角 α angle_alpha	105.41 °
晶胞夹角 β angle_beta	93.97 °
晶胞夹角 γ angle_gamma	104.29 °
晶胞分子数 Z z_pdb	8

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

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	29.970 Å
R 因子 r_factor	0.1860
R_work r_work	0.1836
R_free r_free	0.2322

fit	/app/data/saxs_computation/ie/3iei/3iei.fit
pddf	/app/data/pr_computation/ie/3iei/3iei.pr.out
profile	/app/data/saxs_computation/ie/3iei/3iei.dat