SAXSdb — 1fu1

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fu1
沉积日期 deposition_date	2000-09-13
结构标题 title	CRYSTAL STRUCTURE OF HUMAN XRCC4
关键词 keywords	helix-turn-helix, helix bundle, GENE REGULATION; GENE REGULATION
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	34.13 Å
回转半径 Rg (电子) rg_electron	35.56 Å
零角强度 I(0) i0	34364300.00
分子量 molecular_weight	44787.0 kDa
排除体积 excluded_volume	55580 Å³
包络体积 envelope_volume	78197 Å³
水化壳体积 shell_volume	22048 Å³
包络直径 envelope_diameter	137.1 Å
壳层 Rg shell_rg	34.63 Å
包络 Rg envelope_rg	37.36 Å
形状 Rg shape_rg	35.57 Å
总 Rg total_rg	35.43 Å
总原子数 total_atoms	3116
残基数 n_residues	373
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	90.4 Å
Rg (实空间) rg_real	30.22 Å
Rg 误差 (实空间) rg_real_error	0.28 Å
I(0) (实空间) i0_real	3.2500e+07
I(0) 误差 (实空间) i0_real_error	4.2230e+05
Rg (倒空间) rg_reciprocal	34.50 Å
I(0) (倒空间) i0_reciprocal	34340000.0000
解质量估计 total_estimate	0.6671
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	25.6 Å
偏度 Skewness skewness	0.462
峰度 Kurtosis kurtosis	-0.520
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.7649
最高正则化参数 α highest_alpha	2780000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.004; Oscil: 0.949; Stabil: 0.992; Sysdev: 0.000; Positv: 1.000; Valcen: 0.882; 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	DNA REPAIR PROTEIN XRCC4
分子量 formula_weight	23782.4 kDa
突变 mutation	T135I
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	3177

MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTTAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRFILVLNEKKTKIRSLHNKLLNAAQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	ACETIC ACID
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	61

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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	d1fu1a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.59 — XRCC4, N-terminal domain
超家族 Superfamily superfamily	b.59.1 — XRCC4, N-terminal domain
家族 Family family	b.59.1.1 — XRCC4, N-terminal domain

结构域编号 domain_id	d1fu1a2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.11 — XRCC4, C-terminal oligomerization domain
家族 Family family	h.1.11.1 — XRCC4, C-terminal oligomerization domain

结构域编号 domain_id	d1fu1b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.59 — XRCC4, N-terminal domain
超家族 Superfamily superfamily	b.59.1 — XRCC4, N-terminal domain
家族 Family family	b.59.1.1 — XRCC4, N-terminal domain

结构域编号 domain_id	d1fu1b2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.11 — XRCC4, C-terminal oligomerization domain
家族 Family family	h.1.11.1 — XRCC4, C-terminal oligomerization domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1fu1A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	210 — Dna Repair Protein Xrcc4; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — DNA double-strand break repair and VJ recombination XRCC4, N-terminal

结构域编号 domain_id	1fu1A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	370 —

结构域编号 domain_id	1fu1B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	210 — Dna Repair Protein Xrcc4; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — DNA double-strand break repair and VJ recombination XRCC4, N-terminal

结构域编号 domain_id	1fu1B02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	370 —

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7. 引用文献 (1)

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晶胞边长 a length_a	164.892 Å
晶胞边长 b length_b	74.793 Å
晶胞边长 c length_c	87.307 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.97 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	29.930 Å
R 因子 r_factor	0.2460
R_work r_work	0.2310
R_free r_free	0.2630

fit	/app/data/saxs_computation/fu/1fu1/1fu1.fit
pddf	/app/data/pr_computation/fu/1fu1/1fu1.pr.out
profile	/app/data/saxs_computation/fu/1fu1/1fu1.dat

CRYSTAL STRUCTURE OF HUMAN XRCC4

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