SAXSdb — 1kq4

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1kq4
沉积日期 deposition_date	2002-01-03
结构标题 title	CRYSTAL STRUCTURE OF A THY1-COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA AT 2.25 A RESOLUTION
关键词 keywords	;THY1-COMPLEMENTING PROTEIN, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, TRANSFERASE ;; TRANSFERASE
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	28.74 Å
回转半径 Rg (电子) rg_electron	28.37 Å
零角强度 I(0) i0	159876000.00
分子量 molecular_weight	102400.0 kDa
排除体积 excluded_volume	128400 Å³
包络体积 envelope_volume	150420 Å³
水化壳体积 shell_volume	42785 Å³
包络直径 envelope_diameter	102.1 Å
壳层 Rg shell_rg	36.65 Å
包络 Rg envelope_rg	28.79 Å
形状 Rg shape_rg	28.37 Å
总 Rg total_rg	29.05 Å
总原子数 total_atoms	7193
残基数 n_residues	822
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	96.3 Å
Rg (实空间) rg_real	28.72 Å
Rg 误差 (实空间) rg_real_error	0.59 Å
I(0) (实空间) i0_real	1.5990e+08
I(0) 误差 (实空间) i0_real_error	2.2620e+06
Rg (倒空间) rg_reciprocal	28.73 Å
I(0) (倒空间) i0_reciprocal	159900000.0000
解质量估计 total_estimate	0.8616
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	35.0 Å
偏度 Skewness skewness	0.437
峰度 Kurtosis kurtosis	0.048
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	89900000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.923

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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 TM0449
分子量 formula_weight	27785.1 kDa
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
原子数 atom_count	7467

MGSDKIHHHHHHMKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV

来源 Source

来源生物 organism	Thermotoga maritima
NCBI 分类编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

Entity 2 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 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	274

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1kq4a1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.207 — Thymidylate synthase-complementing protein Thy1
超家族 Superfamily superfamily	d.207.1 — Thymidylate synthase-complementing protein Thy1
家族 Family family	d.207.1.1 — Thymidylate synthase-complementing protein Thy1

结构域编号 domain_id	d1kq4a2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1kq4b_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.207 — Thymidylate synthase-complementing protein Thy1
超家族 Superfamily superfamily	d.207.1 — Thymidylate synthase-complementing protein Thy1
家族 Family family	d.207.1.1 — Thymidylate synthase-complementing protein Thy1

结构域编号 domain_id	d1kq4c_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.207 — Thymidylate synthase-complementing protein Thy1
超家族 Superfamily superfamily	d.207.1 — Thymidylate synthase-complementing protein Thy1
家族 Family family	d.207.1.1 — Thymidylate synthase-complementing protein Thy1

结构域编号 domain_id	d1kq4d_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.207 — Thymidylate synthase-complementing protein Thy1
超家族 Superfamily superfamily	d.207.1 — Thymidylate synthase-complementing protein Thy1
家族 Family family	d.207.1.1 — Thymidylate synthase-complementing protein Thy1

CATH v4.4 (4 domains)

结构域编号 domain_id	1kq4A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	1kq4B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	1kq4C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	1kq4D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	170 —

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7. 引用文献 (1)

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晶胞边长 a length_a	54.200 Å
晶胞边长 b length_b	116.610 Å
晶胞边长 c length_c	141.830 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	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.250 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1920
R_work r_work	0.1920
R_free r_free	0.2400

fit	/app/data/saxs_computation/kq/1kq4/1kq4.fit
pddf	/app/data/pr_computation/kq/1kq4/1kq4.pr.out
profile	/app/data/saxs_computation/kq/1kq4/1kq4.dat

CRYSTAL STRUCTURE OF A THY1-COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA AT 2.25 A RESOLUTION

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