SAXSdb — 1cko

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

MRNA CAPPING ENZYME

Paramecium bursaria Chlorella virus 1

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 1–330	未记录	ZN ZINC ION × 1 GP3 DIGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 6.5；HANGING DROP VAPOR DIFFUSION. 15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 1.3 MM CAP ANALOG (GPPPG) 0.4 M NACL, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 50 MM POTASSIUM PHOSPHATE, 5-10% PEG 8000, 2MM ZNCL2 PH 6.5., vapor diffusion - hanging drop	分辨率 3.10 Å R-free 0.314
2	蛋白同源多聚体同源多聚体蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 A； UniProt 1–330	未记录	ZN ZINC ION × 2 GP3 DIGUANOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 6.5；HANGING DROP VAPOR DIFFUSION. 15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 1.3 MM CAP ANALOG (GPPPG) 0.4 M NACL, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 50 MM POTASSIUM PHOSPHATE, 5-10% PEG 8000, 2MM ZNCL2 PH 6.5., vapor diffusion - hanging drop	分辨率 3.10 Å R-free 0.314

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 1CKO	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
1CKM STRUCTURE OF TWO DIFFERENT CONFORMATIONS OF MRNA CAPPING ENZYME IN COMPLEX WITH GTP 提交 1997-04-20	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 1–330（330 aa）	未记录	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS-HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE 34% MEOPEG 5000, PH 7.5., vapor diffusion - hanging drop	分辨率 2.50 Å R-free 0.299
1CKM STRUCTURE OF TWO DIFFERENT CONFORMATIONS OF MRNA CAPPING ENZYME IN COMPLEX WITH GTP 提交 1997-04-20	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 1–330（330 aa）	未记录	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS-HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE 34% MEOPEG 5000, PH 7.5., vapor diffusion - hanging drop	分辨率 2.50 Å R-free 0.299
1CKM STRUCTURE OF TWO DIFFERENT CONFORMATIONS OF MRNA CAPPING ENZYME IN COMPLEX WITH GTP 提交 1997-04-20	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 3 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–330（330 aa）链 B 1–330（330 aa）	未记录	GTP GUANOSINE-5'-TRIPHOSPHATE × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS-HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE 34% MEOPEG 5000, PH 7.5., vapor diffusion - hanging drop	分辨率 2.50 Å R-free 0.299
1CKM STRUCTURE OF TWO DIFFERENT CONFORMATIONS OF MRNA CAPPING ENZYME IN COMPLEX WITH GTP 提交 1997-04-20	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 4 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 1–330（330 aa）链 B 1–330（330 aa）	未记录	GTP GUANOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS-HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE 34% MEOPEG 5000, PH 7.5., vapor diffusion - hanging drop	分辨率 2.50 Å R-free 0.299
1CKM STRUCTURE OF TWO DIFFERENT CONFORMATIONS OF MRNA CAPPING ENZYME IN COMPLEX WITH GTP 提交 1997-04-20	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 × 2 PDB 声明：dimeric	链 A 1–330（330 aa）	未记录	GTP GUANOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS-HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE 34% MEOPEG 5000, PH 7.5., vapor diffusion - hanging drop	分辨率 2.50 Å R-free 0.299
1CKN STRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP 提交 1997-04-20	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 1–330（330 aa）	未记录	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS- HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE, 34% MEOPEG 5000, PH 7.5. THE CRYSTALS WERE SOAKED IN EQUILIBRATION SOLUTION WITH 100 MM MANGANESE(II)CHLORIDE AND 5 MM GTP FOR 4 HOURS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop	分辨率 2.50 Å R-free 0.299
1CKN STRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP 提交 1997-04-20	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 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 1–330（330 aa）	非标准单体：是（mmCIF未提供具体位点）	MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS- HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE, 34% MEOPEG 5000, PH 7.5. THE CRYSTALS WERE SOAKED IN EQUILIBRATION SOLUTION WITH 100 MM MANGANESE(II)CHLORIDE AND 5 MM GTP FOR 4 HOURS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop	分辨率 2.50 Å R-free 0.299
1CKN STRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP 提交 1997-04-20	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 3 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 1–330（330 aa）链 B 1–330（330 aa）	非标准单体：是（mmCIF未提供具体位点）	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS- HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE, 34% MEOPEG 5000, PH 7.5. THE CRYSTALS WERE SOAKED IN EQUILIBRATION SOLUTION WITH 100 MM MANGANESE(II)CHLORIDE AND 5 MM GTP FOR 4 HOURS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop	分辨率 2.50 Å R-free 0.299
1CKN STRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP 提交 1997-04-20	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 × 2 PDB 声明：dimeric	链 A 1–330（330 aa）	未记录	GTP GUANOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS- HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE, 34% MEOPEG 5000, PH 7.5. THE CRYSTALS WERE SOAKED IN EQUILIBRATION SOLUTION WITH 100 MM MANGANESE(II)CHLORIDE AND 5 MM GTP FOR 4 HOURS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop	分辨率 2.50 Å R-free 0.299

共 2 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	MCE_CHVP1
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–330； UniProt 1–330

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	1cko
沉积日期 deposition_date	1997-09-06
结构标题 title	STRUCTURE OF MRNA CAPPING ENZYME IN COMPLEX WITH THE CAP ANALOG GPPPG
关键词 keywords	MRNA, CAPPING ENZYME, NUCLEOTIDYLTRANSFERASE; CAPPING ENZYME
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	21.89 Å
回转半径 Rg (电子) rg_electron	21.09 Å
零角强度 I(0) i0	22729600.00
分子量 molecular_weight	37187.0 kDa
排除体积 excluded_volume	46953 Å³
包络体积 envelope_volume	56267 Å³
水化壳体积 shell_volume	22365 Å³
包络直径 envelope_diameter	71.6 Å
壳层 Rg shell_rg	27.74 Å
包络 Rg envelope_rg	21.30 Å
形状 Rg shape_rg	21.09 Å
总 Rg total_rg	22.01 Å
总原子数 total_atoms	2613
残基数 n_residues	317
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	69.8 Å
Rg (实空间) rg_real	21.81 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	2.2730e+07
I(0) 误差 (实空间) i0_real_error	3.1120e+05
Rg (倒空间) rg_reciprocal	21.83 Å
I(0) (倒空间) i0_reciprocal	22730000.0000
解质量估计 total_estimate	0.8248
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	26.0 Å
偏度 Skewness skewness	0.255
峰度 Kurtosis kurtosis	-0.411
角度范围 angular_range	— – 0.3650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4992000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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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 (3)

实体 1 Entity 1 polymer

描述 description	MRNA CAPPING ENZYME
分子量 formula_weight	37885.0 kDa
EC 编号 ec_number	2.7.7.50
来源方法 src_method	man
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	2613

MVPPTINTGKNITTERAVLTLNGLQIKLHKVVGESRDDIVAKMKDLAMDDHKFPRLPGPNPVSIERKDFEKLKQNKYVVSEKTDGIRFMMFFTRVFGFKVCTIIDRAMTVYLLPFKNIPRVLFQGSIFDGELCVDIVEKKFAFVLFDAVVVSGVTVSQMDLASRFFAMKRSLKEFKNVPEDPAILRYKEWIPLEHPTIIKDHLKKANAIYHTDGLIIMSVDEPVIYGRNFNLFKLKPGTHHTIDFIIMSEDGTIGIFDPNLRKNVPVGKLDGYYNKGSIVECGFADGTWKYIQGRSDKNQANDRLTYEKTLLNIEENITIDELLDLFKWE

来源 Source

来源生物 organism	Paramecium bursaria Chlorella virus 1
NCBI 分类编号 ncbi_taxonomy_id	10506
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 3 Entity 3 non-polymer

描述 description	DIGUANOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	788.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1ckoa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.6 — DNA ligase/mRNA capping enzyme postcatalytic domain

结构域编号 domain_id	d1ckoa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.142 — ATP-grasp
超家族 Superfamily superfamily	d.142.2 — DNA ligase/mRNA capping enzyme, catalytic domain
家族 Family family	d.142.2.3 — mRNA capping enzyme

CATH v4.4 (3 domains)

结构域编号 domain_id	1ckoA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — DNA ligase/mRNA capping enzyme

结构域编号 domain_id	1ckoA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1ckoA03
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	87 — mRNA Capping Enzyme; Chain
同源超家族 H-superfamily homologous superfamily	10 — mRNA Capping Enzyme; domain 3

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8. 引用文献 (3)

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晶胞边长 a length_a	78.476 Å
晶胞边长 b length_b	164.013 Å
晶胞边长 c length_c	103.502 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	8

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.3140

fit	/app/data/saxs_computation/ck/1cko/1cko.fit
pddf	/app/data/pr_computation/ck/1cko/1cko.pr.out
profile	/app/data/saxs_computation/ck/1cko/1cko.dat

STRUCTURE OF MRNA CAPPING ENZYME IN COMPLEX WITH THE CAP ANALOG GPPPG

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

MRNA CAPPING ENZYME

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