1tez

COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS

Method: X-RAY DIFFRACTION D_max: 191.2 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	1tez
沉积日期 deposition_date	2004-05-26
结构标题 title	COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS
关键词 keywords	PHOTOLYASE; DNA REPAIR; LIGHT-DRIVEN ELECTRON TRANSFER, LYASE-DNA COMPLEX; LYASE/DNA
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	53.52 Å
回转半径 Rg (电子) rg_electron	54.09 Å
零角强度 I(0) i0	888938000.00
分子量 molecular_weight	235550.0 kDa
排除体积 excluded_volume	289050 Å³
包络体积 envelope_volume	395020 Å³
水化壳体积 shell_volume	64435 Å³
包络直径 envelope_diameter	191.0 Å
壳层 Rg shell_rg	51.48 Å
包络 Rg envelope_rg	53.45 Å
形状 Rg shape_rg	54.08 Å
总 Rg total_rg	54.02 Å
总原子数 total_atoms	16592
残基数 n_residues	1952
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	191.2 Å
Rg (实空间) rg_real	54.07 Å
Rg 误差 (实空间) rg_real_error	2.55 Å
I(0) (实空间) i0_real	8.8890e+08
I(0) 误差 (实空间) i0_real_error	1.9740e+07
Rg (倒空间) rg_reciprocal	53.04 Å
I(0) (倒空间) i0_reciprocal	887600000.0000
解质量估计 total_estimate	0.7719
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	46.1 Å
偏度 Skewness skewness	0.566
峰度 Kurtosis kurtosis	-0.443
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	47110000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.573; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.755; Smooth: 0.557

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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 (9)

Entity 1 polymer

描述 description	5'-D(APTPCPGPGPCPT(TCP)PCPGP*C)-3'
分子量 formula_weight	3259.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	I,K
原子数 atom_count	18206

ATCGGCTTCGC

Entity 2 polymer

描述 description	5'-D(PCPGPAPAPGPCPCPGP*A)-3'
分子量 formula_weight	2749.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	J,L

CGAAGCCGA

Entity 3 polymer

描述 description	5'-D(TPCPGPC)-3'
分子量 formula_weight	1166.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	M,O

TCGC

Entity 4 polymer

描述 description	5'-D(PGPCPCPGP*A)-3'
分子量 formula_weight	1505.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	N,P

GCCGA

Entity 5 polymer

描述 description	Deoxyribodipyrimidine photo-lyase type I
分子量 formula_weight	53474.4 kDa
EC 编号 ec_number	4.1.99.3
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D

AAPILFWHRRDLRLSDNIGLAAARAQSAQLIGLFCLDPQILQSADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTAGIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPVATPTELVDLSPEQLTAIAPLLLSELPTLKQLGFDWDGGFPVEPGETAAIARLQEFCDRAIADYDPQRNFPAEAGTSGLSPALKFGAIGIRQAWQAASAAHALSRSDEARNSIRVWQQELAWREFYQHALYHFPSLADGPYRSLWQQFPWENREALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFLTKDLIIDWRRGEQFFMQHLVDGDLAANNGGWQWSASSGMDPKPLRIFNPASQAKKFDATATYIKRWLPELRHVHPKDLISGEITPIERRGYPAPIVNHNLRQKQFKALYNQLKAAI

来源 Source

来源生物 organism	Synechococcus elongatus PCC 6301
NCBI 分类编号 ncbi_taxonomy_id	269084
宿主生物 host_organism	Escherichia coli

Entity 6 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 8 non-polymer

描述 description	8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE
分子量 formula_weight	363.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 9 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	1614

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1teza1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.99 — Cryptochrome/photolyase FAD-binding domain
超家族 Superfamily superfamily	a.99.1 — Cryptochrome/photolyase FAD-binding domain
家族 Family family	a.99.1.1 — Cryptochrome/photolyase FAD-binding domain

结构域编号 domain_id	d1teza2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.28 — Cryptochrome/photolyase, N-terminal domain
超家族 Superfamily superfamily	c.28.1 — Cryptochrome/photolyase, N-terminal domain
家族 Family family	c.28.1.1 — Cryptochrome/photolyase, N-terminal domain

结构域编号 domain_id	d1tezb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.99 — Cryptochrome/photolyase FAD-binding domain
超家族 Superfamily superfamily	a.99.1 — Cryptochrome/photolyase FAD-binding domain
家族 Family family	a.99.1.1 — Cryptochrome/photolyase FAD-binding domain

结构域编号 domain_id	d1tezb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.28 — Cryptochrome/photolyase, N-terminal domain
超家族 Superfamily superfamily	c.28.1 — Cryptochrome/photolyase, N-terminal domain
家族 Family family	c.28.1.1 — Cryptochrome/photolyase, N-terminal domain

结构域编号 domain_id	d1tezc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.99 — Cryptochrome/photolyase FAD-binding domain
超家族 Superfamily superfamily	a.99.1 — Cryptochrome/photolyase FAD-binding domain
家族 Family family	a.99.1.1 — Cryptochrome/photolyase FAD-binding domain

结构域编号 domain_id	d1tezc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.28 — Cryptochrome/photolyase, N-terminal domain
超家族 Superfamily superfamily	c.28.1 — Cryptochrome/photolyase, N-terminal domain
家族 Family family	c.28.1.1 — Cryptochrome/photolyase, N-terminal domain

结构域编号 domain_id	d1tezd1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.99 — Cryptochrome/photolyase FAD-binding domain
超家族 Superfamily superfamily	a.99.1 — Cryptochrome/photolyase FAD-binding domain
家族 Family family	a.99.1.1 — Cryptochrome/photolyase FAD-binding domain

结构域编号 domain_id	d1tezd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.28 — Cryptochrome/photolyase, N-terminal domain
超家族 Superfamily superfamily	c.28.1 — Cryptochrome/photolyase, N-terminal domain
家族 Family family	c.28.1.1 — Cryptochrome/photolyase, N-terminal domain

CATH v4.4 (12 domains)

结构域编号 domain_id	1tezA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

结构域编号 domain_id	1tezA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	80 —

结构域编号 domain_id	1tezA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	579 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	10 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3

结构域编号 domain_id	1tezB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

结构域编号 domain_id	1tezB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	80 —

结构域编号 domain_id	1tezB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	579 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	10 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3

结构域编号 domain_id	1tezC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

结构域编号 domain_id	1tezC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	80 —

结构域编号 domain_id	1tezC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	579 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	10 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3

结构域编号 domain_id	1tezD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

结构域编号 domain_id	1tezD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	80 —

结构域编号 domain_id	1tezD03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	579 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	10 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3

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7. 引用文献 (2)

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晶胞边长 a length_a	173.815 Å
晶胞边长 b length_b	88.505 Å
晶胞边长 c length_c	161.622 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.11 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	1.800 Å
最低分辨率 resolution_low	29.920 Å
R 因子 r_factor	0.2051
R_work r_work	0.2050
R_free r_free	0.2260

fit	/app/data/saxs_computation/te/1tez/1tez.fit
pddf	/app/data/pr_computation/te/1tez/1tez.pr.out
profile	/app/data/saxs_computation/te/1tez/1tez.dat

COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS

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 (9)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

来源 Source

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 water

6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)