1m5h

Formylmethanofuran:tetrahydromethanopterin formyltransferase from Archaeoglobus fulgidus

Method: X-RAY DIFFRACTION D_max: 144.2 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	1m5h
沉积日期 deposition_date	2002-07-09
结构标题 title	Formylmethanofuran:tetrahydromethanopterin formyltransferase from Archaeoglobus fulgidus
关键词 keywords	ALPHA/BETA SANDWICH, 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	44.05 Å
回转半径 Rg (电子) rg_electron	43.75 Å
零角强度 I(0) i0	865569000.00
分子量 molecular_weight	254250.0 kDa
排除体积 excluded_volume	322320 Å³
包络体积 envelope_volume	403280 Å³
水化壳体积 shell_volume	76005 Å³
包络直径 envelope_diameter	145.9 Å
壳层 Rg shell_rg	49.14 Å
包络 Rg envelope_rg	43.25 Å
形状 Rg shape_rg	43.75 Å
总 Rg total_rg	43.99 Å
总原子数 total_atoms	17864
残基数 n_residues	2376
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	144.2 Å
Rg (实空间) rg_real	44.10 Å
Rg 误差 (实空间) rg_real_error	1.03 Å
I(0) (实空间) i0_real	8.6560e+08
I(0) 误差 (实空间) i0_real_error	1.5990e+07
Rg (倒空间) rg_reciprocal	44.05 Å
I(0) (倒空间) i0_reciprocal	865500000.0000
解质量估计 total_estimate	0.8103
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	48.1 Å
偏度 Skewness skewness	0.371
峰度 Kurtosis kurtosis	-0.520
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	159500000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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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	Formylmethanofuran--tetrahydromethanopterin formyltransferase
分子量 formula_weight	31702.2 kDa
EC 编号 ec_number	2.3.1.101
来源方法 src_method	man
拷贝数 entity_count	8

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
原子数 atom_count	19658

MKVNGVEVEETFAEAFDIKIARVLITGYDYYWAWVAANEATGFGTSVIMCPAEAGIEIKAKPSETPDGRPGYYIQICHMSKKGLEEQLLARLGQCVLTAPTTAVFNGLPDAEEKDDTGFKLKFFADGYQKEVEVGGRKCWAVPMMEGDFIIENDIGYTNGIAGGNFFIMAETQPSALAAAKAAVDAISDVEGVITPFPGGIVASGSKVGANKYKFLKASTNEKFAPSIRDQVEGTQIPAGVKAVYEIVINGLNADAIKEATRVGILAATKIPGVVKITAGNYGGKLGKHIINLNELF

来源 Source

来源生物 organism	Archaeoglobus fulgidus
NCBI 分类编号 ncbi_taxonomy_id	2234
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	24

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	1794

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6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

结构域编号 domain_id	d1m5ha1
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5ha2
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5hb1
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5hb2
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5hc1
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5hc2
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5hd1
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5hd2
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5he1
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5he2
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5hf1
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5hf2
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5hg1
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5hg2
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5hh1
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

结构域编号 domain_id	d1m5hh2
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.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
家族 Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

CATH v4.4 (16 domains)

结构域编号 domain_id	1m5hA01
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	520 —

结构域编号 domain_id	1m5hA02
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	520 —

结构域编号 domain_id	1m5hB01
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	520 —

结构域编号 domain_id	1m5hB02
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	520 —

结构域编号 domain_id	1m5hC01
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	520 —

结构域编号 domain_id	1m5hC02
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	520 —

结构域编号 domain_id	1m5hD01
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	520 —

结构域编号 domain_id	1m5hD02
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	520 —

结构域编号 domain_id	1m5hE01
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	520 —

结构域编号 domain_id	1m5hE02
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	520 —

结构域编号 domain_id	1m5hF01
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	520 —

结构域编号 domain_id	1m5hF02
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	520 —

结构域编号 domain_id	1m5hG01
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	520 —

结构域编号 domain_id	1m5hG02
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	520 —

结构域编号 domain_id	1m5hH01
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	520 —

结构域编号 domain_id	1m5hH02
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	520 —

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7. 引用文献 (1)

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晶胞边长 a length_a	77.100 Å
晶胞边长 b length_b	81.810 Å
晶胞边长 c length_c	99.100 Å
晶胞夹角 α angle_alpha	90.10 °
晶胞夹角 β angle_beta	110.04 °
晶胞夹角 γ angle_gamma	93.75 °
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	2.000 Å
最低分辨率 resolution_low	29.250 Å
R 因子 r_factor	0.2290
R_work r_work	0.2290
R_free r_free	0.2820

fit	/app/data/saxs_computation/m5/1m5h/1m5h.fit
pddf	/app/data/pr_computation/m5/1m5h/1m5h.pr.out
profile	/app/data/saxs_computation/m5/1m5h/1m5h.dat