2b5l

Crystal Structure of DDB1 In Complex with Simian Virus 5 V Protein

Method: X-RAY DIFFRACTION D_max: 179.1 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	2b5l
沉积日期 deposition_date	2005-09-28
结构标题 title	Crystal Structure of DDB1 In Complex with Simian Virus 5 V Protein
关键词 keywords	DDB1, SV5-V, beta propeller, propeller cluster, zinc finger, PROTEIN BINDING-VIRAL PROTEIN COMPLEX; PROTEIN BINDING/VIRAL PROTEIN
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	49.54 Å
回转半径 Rg (电子) rg_electron	49.18 Å
零角强度 I(0) i0	1215600000.00
分子量 molecular_weight	290610.0 kDa
排除体积 excluded_volume	363860 Å³
包络体积 envelope_volume	508790 Å³
水化壳体积 shell_volume	85080 Å³
包络直径 envelope_diameter	189.4 Å
壳层 Rg shell_rg	54.25 Å
包络 Rg envelope_rg	48.24 Å
形状 Rg shape_rg	49.18 Å
总 Rg total_rg	49.38 Å
总原子数 total_atoms	20399
残基数 n_residues	2615
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	179.1 Å
Rg (实空间) rg_real	49.46 Å
Rg 误差 (实空间) rg_real_error	1.86 Å
I(0) (实空间) i0_real	1.2160e+09
I(0) 误差 (实空间) i0_real_error	2.3800e+07
Rg (倒空间) rg_reciprocal	49.54 Å
I(0) (倒空间) i0_reciprocal	1216000000.0000
解质量估计 total_estimate	0.8681
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	56.0 Å
偏度 Skewness skewness	0.263
峰度 Kurtosis kurtosis	-0.467
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	121500000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.991

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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	damage-specific DNA binding protein 1
分子量 formula_weight	127117.5 kDa
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	20399

MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRETYDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKDVRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

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	Spodoptera frugiperda

Entity 2 polymer

描述 description	Nonstructural protein V
分子量 formula_weight	23965.0 kDa
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	C,D

MDPTDLSFSPDEINKLIETGLNTVEYFTSQQVTGTSSLGKNTIPPGVTGLLTNAAEAKIQESTNHQKGSVGGGAKPKKPRPKIAIVPADDKTVPGKPIPNPLLGLDSTPSTQTVLDLSGKTLPSGSYKGVKLAKFGKENLMTRFIEEPRENPIATSSPIDFKRGRDTGGFHRREYSIGWVGDEVKVTEWCNPSCSPITAAARRFECTCHQCPVTCSECERDT

来源 Source

来源生物 organism	Simian virus 5
NCBI 分类编号 ncbi_taxonomy_id	11207
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d2b5la1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.4 — WD40 repeat-like
家族 Family family	b.69.4.3 — DDB1-like

结构域编号 domain_id	d2b5la2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.4 — WD40 repeat-like
家族 Family family	b.69.4.3 — DDB1-like

结构域编号 domain_id	d2b5la3
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.297 — DDB1 C-terminal-like
超家族 Superfamily superfamily	a.297.1 — DDB1 C-terminal-like
家族 Family family	a.297.1.1 — DDB1 C-terminal-like

结构域编号 domain_id	d2b5la4
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.4 — WD40 repeat-like
家族 Family family	b.69.4.3 — DDB1-like

结构域编号 domain_id	d2b5lb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.4 — WD40 repeat-like
家族 Family family	b.69.4.3 — DDB1-like

结构域编号 domain_id	d2b5lb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.4 — WD40 repeat-like
家族 Family family	b.69.4.3 — DDB1-like

结构域编号 domain_id	d2b5lb3
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.297 — DDB1 C-terminal-like
超家族 Superfamily superfamily	a.297.1 — DDB1 C-terminal-like
家族 Family family	a.297.1.1 — DDB1 C-terminal-like

结构域编号 domain_id	d2b5lb4
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.4 — WD40 repeat-like
家族 Family family	b.69.4.3 — DDB1-like

结构域编号 domain_id	d2b5lc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.384 — SV5-V core-like
超家族 Superfamily superfamily	d.384.1 — SV5-V core-like
家族 Family family	d.384.1.1 — SV5-V core-like

结构域编号 domain_id	d2b5ld_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.384 — SV5-V core-like
超家族 Superfamily superfamily	d.384.1 — SV5-V core-like
家族 Family family	d.384.1.1 — SV5-V core-like

CATH v4.4 (8 domains)

结构域编号 domain_id	2b5lA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	2b5lA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	2b5lA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	2b5lA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	910 —

结构域编号 domain_id	2b5lB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	2b5lB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	2b5lB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	2b5lB04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	910 —

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7. 引用文献 (1)

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晶胞边长 a length_a	62.758 Å
晶胞边长 b length_b	240.792 Å
晶胞边长 c length_c	117.177 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	101.79 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.850 Å
最低分辨率 resolution_low	47.800 Å
R 因子 r_factor	0.2304
R_work r_work	0.2292
R_free r_free	0.2988

fit	/app/data/saxs_computation/b5/2b5l/2b5l.fit
pddf	/app/data/pr_computation/b5/2b5l/2b5l.pr.out
profile	/app/data/saxs_computation/b5/2b5l/2b5l.dat

Crystal Structure of DDB1 In Complex with Simian Virus 5 V Protein

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

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 non-polymer

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)