SAXSdb — 1oj4

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1oj4
沉积日期 deposition_date	2003-06-30
结构标题 title	Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
关键词 keywords	TRANSFERASE, KINASE, ISOPRENOIDS BIOSYNTHESIS, GHMP KINASE SUPERFAMILY TRANSFERASE; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	27.55 Å
回转半径 Rg (电子) rg_electron	27.38 Å
零角强度 I(0) i0	72007000.00
分子量 molecular_weight	64518.0 kDa
排除体积 excluded_volume	79616 Å³
包络体积 envelope_volume	96242 Å³
水化壳体积 shell_volume	29906 Å³
包络直径 envelope_diameter	97.6 Å
壳层 Rg shell_rg	34.06 Å
包络 Rg envelope_rg	27.34 Å
形状 Rg shape_rg	27.48 Å
总 Rg total_rg	27.70 Å
总原子数 total_atoms	4485
残基数 n_residues	554
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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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	94.5 Å
Rg (实空间) rg_real	27.66 Å
Rg 误差 (实空间) rg_real_error	0.82 Å
I(0) (实空间) i0_real	7.2010e+07
I(0) 误差 (实空间) i0_real_error	1.1400e+06
Rg (倒空间) rg_reciprocal	27.63 Å
I(0) (倒空间) i0_reciprocal	72010000.0000
解质量估计 total_estimate	0.8701
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	29.3 Å
偏度 Skewness skewness	0.467
峰度 Kurtosis kurtosis	-0.206
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	18960000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.956

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

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5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE
分子量 formula_weight	31266.7 kDa
EC 编号 ec_number	2.7.1.148
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	5011

MRTQWPSPAKLNLFLYITGQRADGYHTLQTLFQFLDYGDTISIELRDDGDIRLLTPVEGVEHEDNLIVRAARLLMKTAADSGRLPTGSGANISIDKRLPMGGGLGGGSSNAATVLVALNHLWQCGLSMDELAEMGLTLGADVPVFVRGHAAFAEGVGEILTPVDPPEKWYLVAHPGVSIPTPVIFKDPELPRNTPKRSIETLLKCEFSNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLEQAPEWLNGFVAKGVNLSPLHRAML

来源 Source

来源生物 organism	ESCHERICHIA COLI
NCBI 分类编号 ncbi_taxonomy_id	217992
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
分子量 formula_weight	521.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
分子量 formula_weight	506.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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

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	383

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1oj4a1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.5 — GHMP Kinase, N-terminal domain

结构域编号 domain_id	d1oj4a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.26 — GHMP Kinase, C-terminal domain
家族 Family family	d.58.26.5 — 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE

结构域编号 domain_id	d1oj4b1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.5 — GHMP Kinase, N-terminal domain

结构域编号 domain_id	d1oj4b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.26 — GHMP Kinase, C-terminal domain
家族 Family family	d.58.26.5 — 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE

CATH v4.4 (4 domains)

结构域编号 domain_id	1oj4A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1oj4A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	890 — GHMP kinase, C-terminal domain

结构域编号 domain_id	1oj4B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1oj4B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	890 — GHMP kinase, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	61.000 Å
晶胞边长 b length_b	76.300 Å
晶胞边长 c length_c	68.600 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	107.80 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.010 Å
最低分辨率 resolution_low	65.940 Å
R 因子 r_factor	0.1674
R_work r_work	0.1655
R_free r_free	0.2024

fit	/app/data/saxs_computation/oj/1oj4/1oj4.fit
pddf	/app/data/pr_computation/oj/1oj4/1oj4.pr.out
profile	/app/data/saxs_computation/oj/1oj4/1oj4.dat

Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

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