2fhj

Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes

Method: X-RAY DIFFRACTION D_max: 89.8 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	2fhj
沉积日期 deposition_date	2005-12-25
结构标题 title	Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes
关键词 keywords	tetrahydromethanopterin; methanofuran; C1 metabolism; formyltransferase; complex, 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	30.47 Å
回转半径 Rg (电子) rg_electron	29.06 Å
零角强度 I(0) i0	257971000.00
分子量 molecular_weight	129160.0 kDa
排除体积 excluded_volume	161550 Å³
包络体积 envelope_volume	183510 Å³
水化壳体积 shell_volume	49279 Å³
包络直径 envelope_diameter	94.6 Å
壳层 Rg shell_rg	38.78 Å
包络 Rg envelope_rg	29.13 Å
形状 Rg shape_rg	29.13 Å
总 Rg total_rg	29.68 Å
总原子数 total_atoms	9045
残基数 n_residues	1183
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	89.8 Å
Rg (实空间) rg_real	30.22 Å
Rg 误差 (实空间) rg_real_error	0.40 Å
I(0) (实空间) i0_real	2.5800e+08
I(0) 误差 (实空间) i0_real_error	3.3480e+06
Rg (倒空间) rg_reciprocal	30.33 Å
I(0) (倒空间) i0_reciprocal	258000000.0000
解质量估计 total_estimate	0.9055
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	41.4 Å
偏度 Skewness skewness	0.038
峰度 Kurtosis kurtosis	-0.556
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	110100000.0000
实空间数据点数 n_real_points	53
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: 0.968; Smooth: 0.957

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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 (8)

Entity 1 polymer

描述 description	Formylmethanofuran--tetrahydromethanopterin formyltransferase
分子量 formula_weight	31686.4 kDa
EC 编号 ec_number	2.3.1.101
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	9818

MEINGVEIEDTFAEAFEAKMARVLITAASHKWAMIAVKEATGFGTSVIMCPAEAGIDCGYVPPEETPDGRPGVTIMIGHNDEDELKEQLLDRIGQCVMTAPTASAFDAMPEAEKEDEDRVGYKLSFFGDGYQEEDELDGRKVWKIPVVEGEFIVEDSFGITTGVAGGNFYIMAESQPAGLQAAEAAVDAIKGVEGAYAPFPGGIVASASKVGSKQYDFLPASTNDAYCPTVEDNELPEGVKCVYEIVINGLNEEAVKEAMRVGIEAACQQPGVVKISAGNFGGKLGQYEIHLHDLF

来源 Source

来源生物 organism	Methanopyrus kandleri
NCBI 分类编号 ncbi_taxonomy_id	2320
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Formylmethanofuran--tetrahydromethanopterin formyltransferase
分子量 formula_weight	31702.4 kDa
EC 编号 ec_number	2.3.1.101
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D

来源 Source

来源生物 organism	Methanopyrus kandleri
NCBI 分类编号 ncbi_taxonomy_id	2320
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 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	17

Entity 4 non-polymer

描述 description	N-[4,5,7-TRICARBOXYHEPTANOYL]-L-GAMMA-GLUTAMYL-N-{2-[4-({5-[(FORMYLAMINO)METHYL]-3-FURYL}METHOXY)PHENYL]ETHYL}-D-GLUTAMINE
分子量 formula_weight	776.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 non-polymer

描述 description	;5-(4-{[1-(2-AMINO-5-FORMYL-7-METHYL-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL)ETHYL]AMINO}PHENYL)-5-DEOXY-1-O-{5-O-[(1,3-DICARBOXYPROPOXY)(HYDROXY)PHOSPHORYL]PENTOFURANOSYL}PENTITOL ;
分子量 formula_weight	804.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
分子量 formula_weight	354.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 7 non-polymer

描述 description	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
分子量 formula_weight	634.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 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	451

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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	d2fhja1
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	d2fhja2
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	d2fhjb1
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	d2fhjb2
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	d2fhjc1
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	d2fhjc2
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	d2fhjd1
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	d2fhjd2
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 (8 domains)

结构域编号 domain_id	2fhjA01
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	2fhjA02
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	2fhjB01
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	2fhjB02
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	2fhjC01
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	2fhjC02
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	2fhjD01
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	2fhjD02
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	85.000 Å
晶胞边长 b length_b	74.150 Å
晶胞边长 c length_c	103.870 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	113.54 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	6

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	2.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2210
R_work r_work	0.2190
R_free r_free	0.2560

fit	/app/data/saxs_computation/fh/2fhj/2fhj.fit
pddf	/app/data/pr_computation/fh/2fhj/2fhj.pr.out
profile	/app/data/saxs_computation/fh/2fhj/2fhj.dat

Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes

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

5. 实体与聚合体信息 (8)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)