SAXSdb — 1zel

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1zel
沉积日期 deposition_date	2005-04-19
结构标题 title	Crystal structure of RV2827C protein from Mycobacterium tuberculosis
关键词 keywords	;RV2827C, hypothetical protein, winged-helix, helix-turn-helix, auto-rickshaw, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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	41.08 Å
回转半径 Rg (电子) rg_electron	41.68 Å
零角强度 I(0) i0	63774600.00
分子量 molecular_weight	65128.0 kDa
排除体积 excluded_volume	81985 Å³
包络体积 envelope_volume	111050 Å³
水化壳体积 shell_volume	26009 Å³
包络直径 envelope_diameter	146.7 Å
壳层 Rg shell_rg	38.79 Å
包络 Rg envelope_rg	41.54 Å
形状 Rg shape_rg	41.66 Å
总 Rg total_rg	41.55 Å
总原子数 total_atoms	4597
残基数 n_residues	587
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	138.3 Å
Rg (实空间) rg_real	41.79 Å
Rg 误差 (实空间) rg_real_error	1.80 Å
I(0) (实空间) i0_real	6.3770e+07
I(0) 误差 (实空间) i0_real_error	1.2340e+06
Rg (倒空间) rg_reciprocal	41.08 Å
I(0) (倒空间) i0_reciprocal	63730000.0000
解质量估计 total_estimate	0.6587
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	25.5 Å
偏度 Skewness skewness	0.630
峰度 Kurtosis kurtosis	-0.379
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3762000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.406; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.269; Smooth: 0.073

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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 (6)

Entity 1 polymer

描述 description	hypothetical protein Rv2827c
分子量 formula_weight	32614.5 kDa
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	5021

GAMVVSPAGADRRIPTWASRVVSGLARDRPVVVTKEDLTQRLTEAGCGRDPDSAIRELRRIGWLVQLPVKGTWAFIPPGEAAISDPYLPLRSWLARDQNAGFMLAGASAAWHLGYLDRQPDGRIPIWLPPAKRLPDGLASYVSVVRIPWNAADTALLAPRPALLVRRRLDLVAWATGLPALGPEALLVQIATRPASFGPWADLVPHLDDLVADCSDERLERLLSGRPTSAWQRASYLLDSGGEPARGQALLAKRHTEVMPVTRFTTAHSRDRGESVWAPEYQLVDELVVPLLRVIGKA

来源 Source

来源生物 organism	Mycobacterium tuberculosis
NCBI 分类编号 ncbi_taxonomy_id	83332
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	(4S)-2-METHYL-2,4-PENTANEDIOL
分子量 formula_weight	118.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	FORMIC ACID
分子量 formula_weight	46.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	15

Entity 5 non-polymer

描述 description	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 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	340

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1zela1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.83 — Rv2827c N-terminal domain-like

结构域编号 domain_id	d1zela2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.377 — Rv2827c C-terminal domain-like
超家族 Superfamily superfamily	d.377.1 — Rv2827c C-terminal domain-like
家族 Family family	d.377.1.1 — Rv2827c C-terminal domain-like

结构域编号 domain_id	d1zela3
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	d1zelb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.83 — Rv2827c N-terminal domain-like

结构域编号 domain_id	d1zelb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.377 — Rv2827c C-terminal domain-like
超家族 Superfamily superfamily	d.377.1 — Rv2827c C-terminal domain-like
家族 Family family	d.377.1.1 — Rv2827c C-terminal domain-like

结构域编号 domain_id	d1zelb3
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

CATH v4.4 (2 domains)

结构域编号 domain_id	1zelA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	56 — Phenol Hydroxylase P2 Protein
同源超家族 H-superfamily homologous superfamily	20 — replication protein C, winged helix domain

结构域编号 domain_id	1zelB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	56 — Phenol Hydroxylase P2 Protein
同源超家族 H-superfamily homologous superfamily	20 — replication protein C, winged helix domain

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7. 引用文献 (1)

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晶胞边长 a length_a	87.419 Å
晶胞边长 b length_b	180.653 Å
晶胞边长 c length_c	35.112 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	8

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	1.930 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1827
R_work r_work	0.1814
R_free r_free	0.2245

fit	/app/data/saxs_computation/ze/1zel/1zel.fit
pddf	/app/data/pr_computation/ze/1zel/1zel.pr.out
profile	/app/data/saxs_computation/ze/1zel/1zel.dat

Crystal structure of RV2827C protein from Mycobacterium tuberculosis

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution