SAXSdb — 1jva

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jva
沉积日期 deposition_date	2001-08-29
结构标题 title	CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N AND C EXTEIN PROPEPTIDES
关键词 keywords	PROTEIN-SPLICING, VMA1-DERIVED ENDONUCLEASE, INTEIN, THIAZOLIDINE INTERMEDIATE, VDE, HYDROLASE; HYDROLASE
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	31.34 Å
回转半径 Rg (电子) rg_electron	30.39 Å
零角强度 I(0) i0	142925000.00
分子量 molecular_weight	95896.0 kDa
排除体积 excluded_volume	120510 Å³
包络体积 envelope_volume	151390 Å³
水化壳体积 shell_volume	40832 Å³
包络直径 envelope_diameter	100.6 Å
壳层 Rg shell_rg	38.30 Å
包络 Rg envelope_rg	30.16 Å
形状 Rg shape_rg	30.39 Å
总 Rg total_rg	31.12 Å
总原子数 total_atoms	6755
残基数 n_residues	857
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	97.2 Å
Rg (实空间) rg_real	31.18 Å
Rg 误差 (实空间) rg_real_error	0.46 Å
I(0) (实空间) i0_real	1.4290e+08
I(0) 误差 (实空间) i0_real_error	1.8460e+06
Rg (倒空间) rg_reciprocal	31.25 Å
I(0) (倒空间) i0_reciprocal	142900000.0000
解质量估计 total_estimate	0.9092
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	40.0 Å
偏度 Skewness skewness	0.123
峰度 Kurtosis kurtosis	-0.577
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0005
最高正则化参数 α highest_alpha	29610000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.970

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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 (2)

Entity 1 polymer

描述 description	VMA1-DERIVED HOMING ENDONUCLEASE X10SSS
分子量 formula_weight	53150.1 kDa
EC 编号 ec_number	3.6.1.34
突变 mutation	C284S/H362N/N737S/C738S
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	6960

MSNSDAIIYVGSFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQHRAHKSDSSREVPELLKFTCNATNELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIVELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVTEYAEKLNLCAEYKDRKEPQVAKTVNLYSKVVRGNGIRNNLNTENPLWDAIVGLGFLKDGVKNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVVSVNAEPAKVDMNGTKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFYFELQELKEDDYYGITLSDDSDHQFLLANQVVVHSSGERGNEMAE

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	205

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1jvaa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.86 — Hedgehog/intein (Hint) domain
超家族 Superfamily superfamily	b.86.1 — Hedgehog/intein (Hint) domain
家族 Family family	b.86.1.2 — Intein (protein splicing domain)

结构域编号 domain_id	d1jvaa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.95 — Homing endonuclease-like
超家族 Superfamily superfamily	d.95.2 — Homing endonucleases
家族 Family family	d.95.2.2 — Intein endonuclease

结构域编号 domain_id	d1jvaa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.95 — Homing endonuclease-like
超家族 Superfamily superfamily	d.95.2 — Homing endonucleases
家族 Family family	d.95.2.2 — Intein endonuclease

结构域编号 domain_id	d1jvab1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.86 — Hedgehog/intein (Hint) domain
超家族 Superfamily superfamily	b.86.1 — Hedgehog/intein (Hint) domain
家族 Family family	b.86.1.2 — Intein (protein splicing domain)

结构域编号 domain_id	d1jvab2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.95 — Homing endonuclease-like
超家族 Superfamily superfamily	d.95.2 — Homing endonucleases
家族 Family family	d.95.2.2 — Intein endonuclease

结构域编号 domain_id	d1jvab3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.95 — Homing endonuclease-like
超家族 Superfamily superfamily	d.95.2 — Homing endonucleases
家族 Family family	d.95.2.2 — Intein endonuclease

CATH v4.4 (6 domains)

结构域编号 domain_id	1jvaA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	16 — Endonuclease - Pi-scei; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Hedgehog/Intein (Hint) domain

结构域编号 domain_id	1jvaA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	28 — Endonuclease I-creI
同源超家族 H-superfamily homologous superfamily	10 — Homing endonucleases

结构域编号 domain_id	1jvaA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	28 — Endonuclease I-creI
同源超家族 H-superfamily homologous superfamily	10 — Homing endonucleases

结构域编号 domain_id	1jvaB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	16 — Endonuclease - Pi-scei; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Hedgehog/Intein (Hint) domain

结构域编号 domain_id	1jvaB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	28 — Endonuclease I-creI
同源超家族 H-superfamily homologous superfamily	10 — Homing endonucleases

结构域编号 domain_id	1jvaB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	28 — Endonuclease I-creI
同源超家族 H-superfamily homologous superfamily	10 — Homing endonucleases

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7. 引用文献 (2)

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晶胞边长 a length_a	66.178 Å
晶胞边长 b length_b	68.846 Å
晶胞边长 c length_c	58.524 Å
晶胞夹角 α angle_alpha	103.10 °
晶胞夹角 β angle_beta	98.79 °
晶胞夹角 γ angle_gamma	78.98 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2000
R_work r_work	0.1980
R_free r_free	0.2400

fit	/app/data/saxs_computation/jv/1jva/1jva.fit
pddf	/app/data/pr_computation/jv/1jva/1jva.pr.out
profile	/app/data/saxs_computation/jv/1jva/1jva.dat

CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N AND C EXTEIN PROPEPTIDES

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