1t35

CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN YVDD- A PUTATIVE LYSINE DECARBOXYLASE

Method: X-RAY DIFFRACTION D_max: 106.2 Å Quality: EXCELLENT

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	1t35
沉积日期 deposition_date	2004-04-23
结构标题 title	CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN YVDD- A PUTATIVE LYSINE DECARBOXYLASE
关键词 keywords	;HYPOTHETICAL PROTEIN YVDD, PUTATIVE LYSINE DECARBOXYLASE, STRUCTURAL GENOMICS TARGET, T833, NYSGXRC, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, LYASE ;; LYASE
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	35.84 Å
回转半径 Rg (电子) rg_electron	35.08 Å
零角强度 I(0) i0	453775000.00
分子量 molecular_weight	163420.0 kDa
排除体积 excluded_volume	198660 Å³
包络体积 envelope_volume	253060 Å³
水化壳体积 shell_volume	56801 Å³
包络直径 envelope_diameter	103.2 Å
壳层 Rg shell_rg	44.58 Å
包络 Rg envelope_rg	34.25 Å
形状 Rg shape_rg	35.16 Å
总 Rg total_rg	35.41 Å
总原子数 total_atoms	11088
残基数 n_residues	1346
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	106.2 Å
Rg (实空间) rg_real	35.60 Å
Rg 误差 (实空间) rg_real_error	0.43 Å
I(0) (实空间) i0_real	4.5380e+08
I(0) 误差 (实空间) i0_real_error	5.9520e+06
Rg (倒空间) rg_reciprocal	35.75 Å
I(0) (倒空间) i0_reciprocal	453800000.0000
解质量估计 total_estimate	0.9127
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	50.7 Å
偏度 Skewness skewness	0.003
峰度 Kurtosis kurtosis	-0.711
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0003
最高正则化参数 α highest_alpha	104000000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.967

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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	HYPOTHETICAL PROTEIN YVDD, Putative Lysine Decarboxylase
分子量 formula_weight	21636.9 kDa
EC 编号 ec_number	4.1.1.18
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	11133

MKTICVFAGSNPGGNEAYKRKAAELGVYMAEQGIGLVYGGSRVGLMGTIADAIMENGGTAIGVMPSGLFSGEVVHQNLTELIEVNGMHERKAKMSELADGFISMPGGFGTYEELFEVLCWAQIGIHQKPIGLYNVNGYFEPMMKMVKYSIQEGFSNESHLKLIHSSSRPDELIEQMQNYSYPILEKKWTEI

来源 Source

来源生物 organism	Bacillus subtilis
NCBI 分类编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	14

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	45

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1t35a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.129 — MCP/YpsA-like
超家族 Superfamily superfamily	c.129.1 — MCP/YpsA-like
家族 Family family	c.129.1.1 — MoCo carrier protein-like

结构域编号 domain_id	d1t35b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.129 — MCP/YpsA-like
超家族 Superfamily superfamily	c.129.1 — MCP/YpsA-like
家族 Family family	c.129.1.1 — MoCo carrier protein-like

结构域编号 domain_id	d1t35c_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.129 — MCP/YpsA-like
超家族 Superfamily superfamily	c.129.1 — MCP/YpsA-like
家族 Family family	c.129.1.1 — MoCo carrier protein-like

结构域编号 domain_id	d1t35d_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.129 — MCP/YpsA-like
超家族 Superfamily superfamily	c.129.1 — MCP/YpsA-like
家族 Family family	c.129.1.1 — MoCo carrier protein-like

结构域编号 domain_id	d1t35e_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.129 — MCP/YpsA-like
超家族 Superfamily superfamily	c.129.1 — MCP/YpsA-like
家族 Family family	c.129.1.1 — MoCo carrier protein-like

结构域编号 domain_id	d1t35f_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.129 — MCP/YpsA-like
超家族 Superfamily superfamily	c.129.1 — MCP/YpsA-like
家族 Family family	c.129.1.1 — MoCo carrier protein-like

结构域编号 domain_id	d1t35g_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.129 — MCP/YpsA-like
超家族 Superfamily superfamily	c.129.1 — MCP/YpsA-like
家族 Family family	c.129.1.1 — MoCo carrier protein-like

结构域编号 domain_id	d1t35h_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.129 — MCP/YpsA-like
超家族 Superfamily superfamily	c.129.1 — MCP/YpsA-like
家族 Family family	c.129.1.1 — MoCo carrier protein-like

CATH v4.4 (8 domains)

结构域编号 domain_id	1t35A00
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	450 —

结构域编号 domain_id	1t35B00
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	450 —

结构域编号 domain_id	1t35C00
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	450 —

结构域编号 domain_id	1t35D00
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	450 —

结构域编号 domain_id	1t35E00
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	450 —

结构域编号 domain_id	1t35F00
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	450 —

结构域编号 domain_id	1t35G00
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	450 —

结构域编号 domain_id	1t35H00
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	450 —

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7. 引用文献 (1)

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晶胞边长 a length_a	117.562 Å
晶胞边长 b length_b	170.773 Å
晶胞边长 c length_c	89.721 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	32

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.720 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2430
R_work r_work	0.2430
R_free r_free	0.2860

fit	/app/data/saxs_computation/t3/1t35/1t35.fit
pddf	/app/data/pr_computation/t3/1t35/1t35.pr.out
profile	/app/data/saxs_computation/t3/1t35/1t35.dat