1v9p

Crystal Structure Of Nad+-Dependent DNA Ligase

Method: X-RAY DIFFRACTION D_max: 170.3 Å Quality: REASONABLE

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	1v9p
沉积日期 deposition_date	2004-01-27
结构标题 title	Crystal Structure Of Nad+-Dependent DNA Ligase
关键词 keywords	Nad+-Dependent DNA Ligase, LIGASE; 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	52.41 Å
回转半径 Rg (电子) rg_electron	52.95 Å
零角强度 I(0) i0	268225000.00
分子量 molecular_weight	135200.0 kDa
排除体积 excluded_volume	169480 Å³
包络体积 envelope_volume	268550 Å³
水化壳体积 shell_volume	45294 Å³
包络直径 envelope_diameter	181.1 Å
壳层 Rg shell_rg	49.96 Å
包络 Rg envelope_rg	52.28 Å
形状 Rg shape_rg	52.85 Å
总 Rg total_rg	53.20 Å
总原子数 total_atoms	9530
残基数 n_residues	1168
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	170.3 Å
Rg (实空间) rg_real	52.99 Å
Rg 误差 (实空间) rg_real_error	1.81 Å
I(0) (实空间) i0_real	2.6820e+08
I(0) 误差 (实空间) i0_real_error	5.3040e+06
Rg (倒空间) rg_reciprocal	51.91 Å
I(0) (倒空间) i0_reciprocal	267800000.0000
解质量估计 total_estimate	0.7429
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	51.1 Å
偏度 Skewness skewness	0.524
峰度 Kurtosis kurtosis	-0.572
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8325000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.611; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.786; Smooth: 0.035

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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	DNA ligase
分子量 formula_weight	67321.1 kDa
EC 编号 ec_number	6.5.1.2
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	9768

MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLERALGRKRPFLYTVEHKVDGLSVNLYYEEGVLVFGATRGDGEVGEEVTQNLLTIPTIPRRLKGVPDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLEESGLKSQYELLLWLKEKGFPVEHGYEKALGAEGVEEVYRRFLAQRHALPFEADGVVVKLDDLALWRELGYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGEERPIRWPETCPECGHRLVKEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELLEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESK

来源 Source

来源生物 organism	Thermus filiformis
NCBI 分类编号 ncbi_taxonomy_id	276
宿主生物 host_organism	Escherichia coli

Entity 2 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	2

Entity 3 non-polymer

描述 description	ADENOSINE MONOPHOSPHATE
分子量 formula_weight	347.2 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	238

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1v9pa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.60 — SAM domain-like
超家族 Superfamily superfamily	a.60.2 — RuvA domain 2-like
家族 Family family	a.60.2.2 — NAD+-dependent DNA ligase, domain 3

结构域编号 domain_id	d1v9pa2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.6 — DNA ligase/mRNA capping enzyme postcatalytic domain

结构域编号 domain_id	d1v9pa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.142 — ATP-grasp
超家族 Superfamily superfamily	d.142.2 — DNA ligase/mRNA capping enzyme, catalytic domain
家族 Family family	d.142.2.2 — Adenylation domain of NAD+-dependent DNA ligase

结构域编号 domain_id	d1v9pb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.60 — SAM domain-like
超家族 Superfamily superfamily	a.60.2 — RuvA domain 2-like
家族 Family family	a.60.2.2 — NAD+-dependent DNA ligase, domain 3

结构域编号 domain_id	d1v9pb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.6 — DNA ligase/mRNA capping enzyme postcatalytic domain

结构域编号 domain_id	d1v9pb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.142 — ATP-grasp
超家族 Superfamily superfamily	d.142.2 — DNA ligase/mRNA capping enzyme, catalytic domain
家族 Family family	d.142.2.2 — Adenylation domain of NAD+-dependent DNA ligase

CATH v4.4 (12 domains)

结构域编号 domain_id	1v9pA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	610 — Helix hairpin bin

结构域编号 domain_id	1v9pA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	70 —

结构域编号 domain_id	1v9pA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — DNA ligase/mRNA capping enzyme

结构域编号 domain_id	1v9pA04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1v9pA05
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	20 — 5' to 3' exonuclease, C-terminal subdomain

结构域编号 domain_id	1v9pA06
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	20 — 5' to 3' exonuclease, C-terminal subdomain

结构域编号 domain_id	1v9pB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	610 — Helix hairpin bin

结构域编号 domain_id	1v9pB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	70 —

结构域编号 domain_id	1v9pB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — DNA ligase/mRNA capping enzyme

结构域编号 domain_id	1v9pB04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1v9pB05
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	20 — 5' to 3' exonuclease, C-terminal subdomain

结构域编号 domain_id	1v9pB06
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	20 — 5' to 3' exonuclease, C-terminal subdomain

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7. 引用文献 (1)

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晶胞边长 a length_a	89.210 Å
晶胞边长 b length_b	117.330 Å
晶胞边长 c length_c	97.480 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	115.09 °
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	2.900 Å
最低分辨率 resolution_low	19.930 Å
R 因子 r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.2930

fit	/app/data/saxs_computation/v9/1v9p/1v9p.fit
pddf	/app/data/pr_computation/v9/1v9p/1v9p.pr.out
profile	/app/data/saxs_computation/v9/1v9p/1v9p.dat