2ide

Crystal Structure of the molybdenum cofactor biosynthesis protein C (TTHA1789) from Thermus Theromophilus HB8

Method: X-RAY DIFFRACTION D_max: 122.1 Å Quality: GOOD

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	2ide
沉积日期 deposition_date	2006-09-15
结构标题 title	Crystal Structure of the molybdenum cofactor biosynthesis protein C (TTHA1789) from Thermus Theromophilus HB8
关键词 keywords	;MOAC, MOLYBDENUM COFACTOR (MOCO), MOCO BIOSYNTHESIS, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, BIOSYNTHETIC PROTEIN ;; BIOSYNTHETIC PROTEIN
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	38.95 Å
回转半径 Rg (电子) rg_electron	38.51 Å
零角强度 I(0) i0	520551000.00
分子量 molecular_weight	189860.0 kDa
排除体积 excluded_volume	239800 Å³
包络体积 envelope_volume	290480 Å³
水化壳体积 shell_volume	61186 Å³
包络直径 envelope_diameter	121.3 Å
壳层 Rg shell_rg	45.79 Å
包络 Rg envelope_rg	38.33 Å
形状 Rg shape_rg	38.53 Å
总 Rg total_rg	38.80 Å
总原子数 total_atoms	13266
残基数 n_residues	1769
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	122.1 Å
Rg (实空间) rg_real	38.95 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	5.2060e+08
I(0) 误差 (实空间) i0_real_error	9.0230e+06
Rg (倒空间) rg_reciprocal	38.96 Å
I(0) (倒空间) i0_reciprocal	520600000.0000
解质量估计 total_estimate	0.8793
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	41.7 Å
偏度 Skewness skewness	0.308
峰度 Kurtosis kurtosis	-0.616
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	162300000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.696

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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 (3)

Entity 1 polymer

描述 description	Molybdenum cofactor biosynthesis protein C
分子量 formula_weight	16946.7 kDa
来源方法 src_method	man
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	14850

MDLTHFQDGRPRMVDVTEKPETFRTATAEAFVELTEEALSALEKGGVGKGDPLVVAQLAGILAAKKTADLIPLCHPLPLTGVEVRVELLKAEKRVRIEATVKTKAETGVEMEAMTACAVAALTVYDMLKAASKGLVISQVRLLHKAGGKSGEWRREQ

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	300852
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 3 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	1584

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d2idea_
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.58.21 — Molybdenum cofactor biosynthesis protein C, MoaC
家族 Family family	d.58.21.0 — automated matches

结构域编号 domain_id	d2ideb_
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.58.21 — Molybdenum cofactor biosynthesis protein C, MoaC
家族 Family family	d.58.21.0 — automated matches

结构域编号 domain_id	d2idec_
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.58.21 — Molybdenum cofactor biosynthesis protein C, MoaC
家族 Family family	d.58.21.0 — automated matches

结构域编号 domain_id	d2ided_
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.58.21 — Molybdenum cofactor biosynthesis protein C, MoaC
家族 Family family	d.58.21.0 — automated matches

结构域编号 domain_id	d2idee_
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.58.21 — Molybdenum cofactor biosynthesis protein C, MoaC
家族 Family family	d.58.21.0 — automated matches

结构域编号 domain_id	d2idef_
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.58.21 — Molybdenum cofactor biosynthesis protein C, MoaC
家族 Family family	d.58.21.0 — automated matches

结构域编号 domain_id	d2ideg_
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.58.21 — Molybdenum cofactor biosynthesis protein C, MoaC
家族 Family family	d.58.21.0 — automated matches

结构域编号 domain_id	d2ideh_
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.58.21 — Molybdenum cofactor biosynthesis protein C, MoaC
家族 Family family	d.58.21.0 — automated matches

结构域编号 domain_id	d2idei_
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.58.21 — Molybdenum cofactor biosynthesis protein C, MoaC
家族 Family family	d.58.21.0 — automated matches

结构域编号 domain_id	d2idej_
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.58.21 — Molybdenum cofactor biosynthesis protein C, MoaC
家族 Family family	d.58.21.0 — automated matches

结构域编号 domain_id	d2idek_
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.58.21 — Molybdenum cofactor biosynthesis protein C, MoaC
家族 Family family	d.58.21.0 — automated matches

结构域编号 domain_id	d2idel_
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.58.21 — Molybdenum cofactor biosynthesis protein C, MoaC
家族 Family family	d.58.21.0 — automated matches

CATH v4.4 (12 domains)

结构域编号 domain_id	2ideA00
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	640 — Molybdopterin cofactor biosynthesis C (MoaC) domain

结构域编号 domain_id	2ideB00
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	640 — Molybdopterin cofactor biosynthesis C (MoaC) domain

结构域编号 domain_id	2ideC00
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	640 — Molybdopterin cofactor biosynthesis C (MoaC) domain

结构域编号 domain_id	2ideD00
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	640 — Molybdopterin cofactor biosynthesis C (MoaC) domain

结构域编号 domain_id	2ideE00
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	640 — Molybdopterin cofactor biosynthesis C (MoaC) domain

结构域编号 domain_id	2ideF00
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	640 — Molybdopterin cofactor biosynthesis C (MoaC) domain

结构域编号 domain_id	2ideG00
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	640 — Molybdopterin cofactor biosynthesis C (MoaC) domain

结构域编号 domain_id	2ideH00
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	640 — Molybdopterin cofactor biosynthesis C (MoaC) domain

结构域编号 domain_id	2ideI00
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	640 — Molybdopterin cofactor biosynthesis C (MoaC) domain

结构域编号 domain_id	2ideJ00
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	640 — Molybdopterin cofactor biosynthesis C (MoaC) domain

结构域编号 domain_id	2ideK00
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	640 — Molybdopterin cofactor biosynthesis C (MoaC) domain

结构域编号 domain_id	2ideL00
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	640 — Molybdopterin cofactor biosynthesis C (MoaC) domain

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7. 引用文献 (1)

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晶胞边长 a length_a	64.809 Å
晶胞边长 b length_b	109.836 Å
晶胞边长 c length_c	115.192 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	104.86 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

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	1.900 Å
最低分辨率 resolution_low	49.660 Å
R 因子 r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2260

fit	/app/data/saxs_computation/id/2ide/2ide.fit
pddf	/app/data/pr_computation/id/2ide/2ide.pr.out
profile	/app/data/saxs_computation/id/2ide/2ide.dat