SAXSdb — 1ik9

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ik9
沉积日期 deposition_date	2001-05-03
结构标题 title	CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX
关键词 keywords	;DNA end joining, double-strand break repair, V(D)J recombination, protein-protein complex, coiled coil, GENE REGULATION-LIGASE COMPLEX ;; GENE REGULATION/LIGASE
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	41.41 Å
回转半径 Rg (电子) rg_electron	42.51 Å
零角强度 I(0) i0	38397700.00
分子量 molecular_weight	49741.0 kDa
排除体积 excluded_volume	62494 Å³
包络体积 envelope_volume	94542 Å³
水化壳体积 shell_volume	22278 Å³
包络直径 envelope_diameter	149.2 Å
壳层 Rg shell_rg	39.02 Å
包络 Rg envelope_rg	42.17 Å
形状 Rg shape_rg	42.47 Å
总 Rg total_rg	42.37 Å
总原子数 total_atoms	3512
残基数 n_residues	430
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	152.3 Å
Rg (实空间) rg_real	42.22 Å
Rg 误差 (实空间) rg_real_error	2.58 Å
I(0) (实空间) i0_real	3.8400e+07
I(0) 误差 (实空间) i0_real_error	8.7250e+05
Rg (倒空间) rg_reciprocal	41.41 Å
I(0) (倒空间) i0_reciprocal	38360000.0000
解质量估计 total_estimate	0.6523
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	24.1 Å
偏度 Skewness skewness	0.618
峰度 Kurtosis kurtosis	-0.581
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1717000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.212; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.107; Smooth: 0.734

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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	24466.6 kDa
突变 mutation	C93A,C128A,C130A,C165A
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	3736

MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESAYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELIAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALETDLYKRFILVLNEKKTKIRSLHNKLLNAAQEREKDIKQEG

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 BL21(DE3)

Entity 2 polymer

描述 description	DNA LIGASE IV
分子量 formula_weight	4323.7 kDa
EC 编号 ec_number	6.5.1.1
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	C

PSTKEHFAREYDCYGDSYFIDTDLNQLKEVFSGIKNS

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 BL21(DE3)

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	224

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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	d1ik9a1
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	d1ik9a2
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	d1ik9b1
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	d1ik9b2
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	1ik9A01
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	1ik9A02
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	1ik9B01
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	1ik9B02
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	45.062 Å
晶胞边长 b length_b	79.628 Å
晶胞边长 c length_c	242.142 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	2.300 Å
最低分辨率 resolution_low	33.260 Å
R 因子 r_factor	—
R_work r_work	0.2280
R_free r_free	0.2660

fit	/app/data/saxs_computation/ik/1ik9/1ik9.fit
pddf	/app/data/pr_computation/ik/1ik9/1ik9.pr.out
profile	/app/data/saxs_computation/ik/1ik9/1ik9.dat

CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)