SAXSdb — 1qd1

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1qd1
沉积日期 deposition_date	1999-07-08
结构标题 title	THE CRYSTAL STRUCTURE OF THE FORMIMINOTRANSFERASE DOMAIN OF FORMIMINOTRANSFERASE-CYCLODEAMINASE.
关键词 keywords	FUNCTIONAL DIMER, ALPHA-BETA-BETA-ALPHA SANDWICH, ELECTROSTATICALLY CHARGED SUBSTRATE TUNNEL, 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	29.98 Å
回转半径 Rg (电子) rg_electron	29.30 Å
零角强度 I(0) i0	83186900.00
分子量 molecular_weight	72110.0 kDa
排除体积 excluded_volume	90305 Å³
包络体积 envelope_volume	108790 Å³
水化壳体积 shell_volume	31820 Å³
包络直径 envelope_diameter	104.3 Å
壳层 Rg shell_rg	35.59 Å
包络 Rg envelope_rg	29.16 Å
形状 Rg shape_rg	29.30 Å
总 Rg total_rg	29.86 Å
总原子数 total_atoms	5080
残基数 n_residues	644
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	98.2 Å
Rg (实空间) rg_real	30.11 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	8.3190e+07
I(0) 误差 (实空间) i0_real_error	1.2510e+06
Rg (倒空间) rg_reciprocal	30.06 Å
I(0) (倒空间) i0_reciprocal	83180000.0000
解质量估计 total_estimate	0.8677
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	27.8 Å
偏度 Skewness skewness	0.425
峰度 Kurtosis kurtosis	-0.482
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	27310000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.911; Smooth: 0.808

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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	FORMIMINOTRANSFERASE-CYCLODEAMINASE
分子量 formula_weight	35878.9 kDa
EC 编号 ec_number	2.1.2.5
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	6042

SQLVECVPNFSEGKNQEVIDAISRAVAQTPGCVLLDVDSGPSTNRTVYTFVGRPEDVVEGALNAARAAYQLIDMSRHHGEHPRMGALDVCPFIPVRGVTMDECVRCAQAFGQRLAEELGVPVYLYGEAARTAGRQSLPALRAGEYEALPEKLKQAEWAPDFGPSAFVPSWGATVAGARKFLLAFNINLLSTREQAHRIALDLREQGRGKDQPGRLKKVQAIGWYLDEKNLAQVSTNLLDFEVTGLHTVFEETCREAQELSLPVVGSQLVGLVPLKALLDAAAFYCEKENLFLLQDEHRIRLVVNRLGLDSLAPFKPKERIIEYLV

来源 Source

来源生物 organism	Sus scrofa
通用名 common_name	pig
NCBI 分类编号 ncbi_taxonomy_id	9823
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid
分子量 formula_weight	473.4 kDa
突变 mutation	PRODUCT ANALOGUE OF THE NATURAL SUBSTRATE
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	771

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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	d1qd1a1
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.58.34 — Formiminotransferase domain of formiminotransferase-cyclodeaminase.
家族 Family family	d.58.34.1 — Formiminotransferase domain of formiminotransferase-cyclodeaminase.

结构域编号 domain_id	d1qd1a2
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.58.34 — Formiminotransferase domain of formiminotransferase-cyclodeaminase.
家族 Family family	d.58.34.1 — Formiminotransferase domain of formiminotransferase-cyclodeaminase.

结构域编号 domain_id	d1qd1b1
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.58.34 — Formiminotransferase domain of formiminotransferase-cyclodeaminase.
家族 Family family	d.58.34.1 — Formiminotransferase domain of formiminotransferase-cyclodeaminase.

结构域编号 domain_id	d1qd1b2
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.58.34 — Formiminotransferase domain of formiminotransferase-cyclodeaminase.
家族 Family family	d.58.34.1 — Formiminotransferase domain of formiminotransferase-cyclodeaminase.

CATH v4.4 (4 domains)

结构域编号 domain_id	1qd1A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	990 — Formiminotransferase-cyclodeaminase; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Formiminotransferase, N-terminal subdomain

结构域编号 domain_id	1qd1A02
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	670 — Formiminotransferase, C-terminal subdomain

结构域编号 domain_id	1qd1B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	990 — Formiminotransferase-cyclodeaminase; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Formiminotransferase, N-terminal subdomain

结构域编号 domain_id	1qd1B02
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	670 — Formiminotransferase, C-terminal subdomain

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7. 引用文献 (1)

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晶胞边长 a length_a	64.310 Å
晶胞边长 b length_b	103.840 Å
晶胞边长 c length_c	122.770 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	8

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	1.700 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	—
R_work r_work	0.1910
R_free r_free	0.2130

fit	/app/data/saxs_computation/qd/1qd1/1qd1.fit
pddf	/app/data/pr_computation/qd/1qd1/1qd1.pr.out
profile	/app/data/saxs_computation/qd/1qd1/1qd1.dat

THE CRYSTAL STRUCTURE OF THE FORMIMINOTRANSFERASE DOMAIN OF FORMIMINOTRANSFERASE-CYCLODEAMINASE.

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution