1v8c

Crystal Structure of MoaD related protein from Thermus thermophilus HB8

Method: X-RAY DIFFRACTION D_max: 80.7 Å Quality: EXCELLENT

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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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1v8c
沉积日期 deposition_date	2004-01-05
结构标题 title	Crystal Structure of MoaD related protein from Thermus thermophilus HB8
关键词 keywords	MoaD related protein, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, PROTEIN BINDING; PROTEIN BINDING
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	27.39 Å
回转半径 Rg (电子) rg_electron	26.01 Å
零角强度 I(0) i0	82276900.00
分子量 molecular_weight	72959.0 kDa
排除体积 excluded_volume	92253 Å³
包络体积 envelope_volume	113890 Å³
水化壳体积 shell_volume	35617 Å³
包络直径 envelope_diameter	82.4 Å
壳层 Rg shell_rg	34.05 Å
包络 Rg envelope_rg	25.71 Å
形状 Rg shape_rg	26.00 Å
总 Rg total_rg	26.94 Å
总原子数 total_atoms	5175
残基数 n_residues	655
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	80.7 Å
Rg (实空间) rg_real	27.18 Å
Rg 误差 (实空间) rg_real_error	0.35 Å
I(0) (实空间) i0_real	8.2280e+07
I(0) 误差 (实空间) i0_real_error	9.9650e+05
Rg (倒空间) rg_reciprocal	27.24 Å
I(0) (倒空间) i0_reciprocal	82280000.0000
解质量估计 total_estimate	0.9043
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	37.6 Å
偏度 Skewness skewness	0.098
峰度 Kurtosis kurtosis	-0.465
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	57380000.0000
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: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.932

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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 (4)

Entity 1 polymer

描述 description	MoaD related protein
分子量 formula_weight	18530.9 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	5741

PKVNLYATFRDLTGKSQLELPGATVGEVLENLVRAYPALKEELFEGEGLAERVSVFLEGRDVRYLQGLSTPLSPGATLDLFPPVAGGGFERTFGAFPPWLLERYLEEWGGTREGEGVYRLPGAVVRFREVEPLKVGSLSIPQLRVEVEGEEAERWFERIAFAASRGGG

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	2

Entity 3 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	558

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1v8ca1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.3 — MoaD/ThiS
家族 Family family	d.15.3.1 — MoaD

结构域编号 domain_id	d1v8ca2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.5 — MoaD-related protein, C-terminal domain
家族 Family family	d.129.5.1 — MoaD-related protein, C-terminal domain

结构域编号 domain_id	d1v8cb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.3 — MoaD/ThiS
家族 Family family	d.15.3.1 — MoaD

结构域编号 domain_id	d1v8cb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.5 — MoaD-related protein, C-terminal domain
家族 Family family	d.129.5.1 — MoaD-related protein, C-terminal domain

结构域编号 domain_id	d1v8cc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.3 — MoaD/ThiS
家族 Family family	d.15.3.1 — MoaD

结构域编号 domain_id	d1v8cc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.5 — MoaD-related protein, C-terminal domain
家族 Family family	d.129.5.1 — MoaD-related protein, C-terminal domain

结构域编号 domain_id	d1v8cd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.3 — MoaD/ThiS
家族 Family family	d.15.3.1 — MoaD

结构域编号 domain_id	d1v8cd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.5 — MoaD-related protein, C-terminal domain
家族 Family family	d.129.5.1 — MoaD-related protein, C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1v8cA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	30 — Beta-grasp domain

结构域编号 domain_id	1v8cA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	80 — Molybdopterin cofactor biosynthesis MoaD-related, C-terminal domain

结构域编号 domain_id	1v8cB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	30 — Beta-grasp domain

结构域编号 domain_id	1v8cB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	80 — Molybdopterin cofactor biosynthesis MoaD-related, C-terminal domain

结构域编号 domain_id	1v8cC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	30 — Beta-grasp domain

结构域编号 domain_id	1v8cC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	80 — Molybdopterin cofactor biosynthesis MoaD-related, C-terminal domain

结构域编号 domain_id	1v8cD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	30 — Beta-grasp domain

结构域编号 domain_id	1v8cD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	80 — Molybdopterin cofactor biosynthesis MoaD-related, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	80.179 Å
晶胞边长 b length_b	83.553 Å
晶胞边长 c length_c	93.066 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	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.600 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2210
R_work r_work	0.2210
R_free r_free	0.2470

fit	/app/data/saxs_computation/v8/1v8c/1v8c.fit
pddf	/app/data/pr_computation/v8/1v8c/1v8c.pr.out
profile	/app/data/saxs_computation/v8/1v8c/1v8c.dat