1qd7

PARTIAL MODEL FOR 30S RIBOSOMAL SUBUNIT

Method: X-RAY DIFFRACTION D_max: 194.2 Å Quality: GOOD

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	1qd7
沉积日期 deposition_date	1999-07-09
结构标题 title	PARTIAL MODEL FOR 30S RIBOSOMAL SUBUNIT
关键词 keywords	30S RIBOSOMAL SUBUNIT, LOW RESOLUTION MODEL, RIBOSOME; RIBOSOME
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	57.94 Å
回转半径 Rg (电子) rg_electron	60.77 Å
零角强度 I(0) i0	321647000.00
分子量 molecular_weight	118680.0 kDa
排除体积 excluded_volume	143190 Å³
包络体积 envelope_volume	279180 Å³
水化壳体积 shell_volume	48286 Å³
包络直径 envelope_diameter	205.0 Å
壳层 Rg shell_rg	49.33 Å
包络 Rg envelope_rg	52.13 Å
形状 Rg shape_rg	58.21 Å
总 Rg total_rg	60.42 Å
总原子数 total_atoms	359
残基数 n_residues	359
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	194.2 Å
Rg (实空间) rg_real	58.10 Å
Rg 误差 (实空间) rg_real_error	1.84 Å
I(0) (实空间) i0_real	3.2160e+08
I(0) 误差 (实空间) i0_real_error	6.1450e+06
Rg (倒空间) rg_reciprocal	57.78 Å
I(0) (倒空间) i0_reciprocal	321500000.0000
解质量估计 total_estimate	0.8914
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	79.1 Å
偏度 Skewness skewness	0.320
峰度 Kurtosis kurtosis	-0.214
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	21200000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.872

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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 (10)

Entity 1 polymer

描述 description	CENTRAL FRAGMENT OF 16 S RNA
分子量 formula_weight	53096.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	A
原子数 atom_count	1305

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Entity 2 polymer

描述 description	END FRAGMENT OF 16 S RNA
分子量 formula_weight	17211.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	B

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Entity 3 polymer

描述 description	S4 RIBOSOMAL PROTEIN
分子量 formula_weight	18624.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

MKLSEYGLQLQEKQKLRHMYGVNERQFRKTFEEAGKMPGKHGENFMILLESRLDNLVYRLGLARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQTIAVREKSRNLQVIKEALEANNYIPDYLSFDPEKMEGTYTRLPERSELPAEINEALIVEFYSR

Entity 4 polymer

描述 description	S5 RIBOSOMAL PROTEIN
分子量 formula_weight	15240.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D

INPNKLELEERVVAVNRVAKVVKGGRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIRKAIEDAKKNLIEVPIVGTTIPHEVIGHFGAGEIILKPASEGTGVIAGGPARAVLELAGISDILSKSIGSNTPINMVRATFDGLKQLK

Entity 5 polymer

描述 description	S6 RIBOSOMAL PROTEIN
分子量 formula_weight	11619.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E

MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPF

Entity 6 polymer

描述 description	S7 RIBOSOMAL PROTEIN
分子量 formula_weight	15342.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	F

LQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAE

Entity 7 polymer

描述 description	S8 RIBOSOMAL PROTEIN
分子量 formula_weight	15624.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G

TDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW

Entity 8 polymer

描述 description	S15 RIBOSOMAL PROTEIN
分子量 formula_weight	10200.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H

LTQERKREIIEQFKVHENDTGSPEVQIAILTEQINNLNEHLRVHKKDHHSRRGLLKMVGKRRRLLAYLRNKDVARYREIVEKLGL

Entity 9 polymer

描述 description	S17 RIBOSOMAL PROTEIN
分子量 formula_weight	10081.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	I

QRKVYVGRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMETRPLSATKRFRLVEIVEKAVRAGAGAGAA

Entity 10 polymer

描述 description	S20 RIBOSOMAL PROTEIN
分子量 formula_weight	8528.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	J

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d1qd7c1
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
家族 Family family	i.1.1.3 — Small subunit

结构域编号 domain_id	d1qd7c2
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	d1qd7d_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
家族 Family family	i.1.1.3 — Small subunit

结构域编号 domain_id	d1qd7e_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
家族 Family family	i.1.1.3 — Small subunit

结构域编号 domain_id	d1qd7f_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
家族 Family family	i.1.1.3 — Small subunit

结构域编号 domain_id	d1qd7g_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
家族 Family family	i.1.1.3 — Small subunit

结构域编号 domain_id	d1qd7h_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
家族 Family family	i.1.1.3 — Small subunit

结构域编号 domain_id	d1qd7i_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
家族 Family family	i.1.1.3 — Small subunit

结构域编号 domain_id	d1qd7j_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
家族 Family family	i.1.1.3 — Small subunit

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7. 引用文献 (8)

Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution.

Nature (1999)

PMID: 10476960 · DOI: 10.1038/23631 PRIMARY

;The crystal structure of ribosomal protein S4 reveals a two-domain molecule with an extensive RNA-binding surface: one domain shows structural homology to the ETS DNA-binding motif ;

Embo J. (1998)

DOI: 10.1093/emboj/17.16.4545

;Crystal structure of ribosomal protein S8 from Thermus thermophilus reveals a high degree of structural conservation of a specific RNA binding site ;

J.Mol.Biol. (1998)

DOI: 10.1006/jmbi.1998.1758

Conformational variability of the N-terminal helix in the structure of ribosomal protein S15

Structure (1998)

The structure of ribosomal protein S7 at 1.9 A resolution reveals a beta- hairpin motif that binds double-stranded nucleic acids

Structure (1997)

DOI: 10.1016/S0969-2126(97)00269-4

Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy

Biochemistry (1996)

DOI: 10.1021/bi951062i

Crystal structure of the ribosomal protein S6 from Thermus thermophilus

Embo J. (1994)

The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA

Nature (1992)

DOI: 10.1038/358768a0

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晶胞边长 a length_a	401.600 Å
晶胞边长 b length_b	401.600 Å
晶胞边长 c length_c	174.500 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 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	5.500 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/qd/1qd7/1qd7.fit
pddf	/app/data/pr_computation/qd/1qd7/1qd7.pr.out
profile	/app/data/saxs_computation/qd/1qd7/1qd7.dat

PARTIAL MODEL FOR 30S RIBOSOMAL SUBUNIT

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

5. 实体与聚合体信息 (10)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

Entity 8 polymer

聚合体 Polymer

Entity 9 polymer

聚合体 Polymer

Entity 10 polymer

聚合体 Polymer

6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (9 domains)

7. 引用文献 (8)

8. 文件与曲线 (10)

Files (7)

Curves (3)