1lra

;CRYSTALLOGRAPHIC STUDY OF GLU 58 ALA RNASE T1(ASTERISK)2'-GUANOSINE MONOPHOSPHATE AT 1.9 ANGSTROMS RESOLUTION ;

Method: X-RAY DIFFRACTION D_max: 41.8 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	1lra
沉积日期 deposition_date	1993-10-01
结构标题 title	;CRYSTALLOGRAPHIC STUDY OF GLU 58 ALA RNASE T1(ASTERISK)2'-GUANOSINE MONOPHOSPHATE AT 1.9 ANGSTROMS RESOLUTION ;
关键词 keywords	HYDROLASE(ENDORIBONUCLEASE); HYDROLASE(ENDORIBONUCLEASE)
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	13.81 Å
回转半径 Rg (电子) rg_electron	12.33 Å
零角强度 I(0) i0	3210570.00
分子量 molecular_weight	11354.0 kDa
排除体积 excluded_volume	13611 Å³
包络体积 envelope_volume	15116 Å³
水化壳体积 shell_volume	10434 Å³
包络直径 envelope_diameter	39.4 Å
壳层 Rg shell_rg	18.08 Å
包络 Rg envelope_rg	12.62 Å
形状 Rg shape_rg	12.28 Å
总 Rg total_rg	13.65 Å
总原子数 total_atoms	798
残基数 n_residues	104
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	41.8 Å
Rg (实空间) rg_real	13.69 Å
Rg 误差 (实空间) rg_real_error	0.19 Å
I(0) (实空间) i0_real	3.2110e+06
I(0) 误差 (实空间) i0_real_error	3.2660e+04
Rg (倒空间) rg_reciprocal	13.70 Å
I(0) (倒空间) i0_reciprocal	3211000.0000
解质量估计 total_estimate	0.8979
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	41.2 Å
偏度 Skewness skewness	0.026
峰度 Kurtosis kurtosis	-0.463
角度范围 angular_range	— – 0.5000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	739400.0000
实空间数据点数 n_real_points	80
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.969

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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 (4)

Entity 1 polymer

描述 description	RIBONUCLEASE T1
分子量 formula_weight	11036.7 kDa
EC 编号 ec_number	3.1.27.3
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	896

ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYAWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT

来源 Source

来源生物 organism	Aspergillus oryzae
NCBI 分类编号 ncbi_taxonomy_id	5062

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	1

Entity 3 non-polymer

描述 description	GUANOSINE-2'-MONOPHOSPHATE
分子量 formula_weight	363.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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	90

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1lraa_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.1 — Microbial ribonucleases
超家族 Superfamily superfamily	d.1.1 — Microbial ribonucleases
家族 Family family	d.1.1.4 — Fungal ribonucleases

CATH v4.4 (1 domains)

结构域编号 domain_id	1lraA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	30 — Microbial ribonucleases

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7. 引用文献 (10)

;Crystallographic study of Glu58Ala RNase T1 x 2'-guanosine monophosphate at 1.9-A resolution. ;

Biochemistry (1994)

PMID: 7906540 · DOI: 10.1021/bi00173a006 PRIMARY

Ribonuclease T1 with Free Recognition and Catalytic Site: Crystal Structure Analysis at 1.5 Angstroms

J.Mol.Biol. (1991)

Histidine-40 of Ribonuclease T1Acts as Base Catalyst When the True Catalytic Base, Glutamic Acid 58 is Replaced by Alanine

Biochemistry (1990)

;Three-Dimensional Structure of Ribonuclease T1 Complexed with Guanylyl-2',5'-Guanosine at 1.8 Angstroms Resolution ;

J.Mol.Biol. (1989)

;Three-Dimensional Structure of the Ribonuclease T1(Asterisk)2'-Gmp Complex at 1.9-Angstroms Resolution ;

J.Biol.Chem. (1988)

;Restrained Least-Squares Refinement of the Crystal Structure of the Ribonuclease T1(Asterisk)2'-Guanylic Acid Complex at 1.9 Angstroms Resolution ;

Acta Crystallogr.,Sect.B (1987)

The Structural and Sequence Homology of a Family of Microbial Ribonucleases

Trends Biochem.Sci.(Pers. Ed.) (1983)

Crystallographic Study of Mechanism of Ribonuclease T1-Catalysed Specific RNA Hydrolysis

J.Biomol.Struct.Dyn. (1983)

;Specific Protein-Nucleic Acid Recognition in Ribonuclease T1-2'-Guanylic Acid Complex. An X-Ray Study ;

Nature (1982)

;Crystallization of a Complex between Ribonuclease T1 and 2'-Guanylic Acid ;

Eur.J.Biochem. (1980)

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晶胞边长 a length_a	32.440 Å
晶胞边长 b length_b	49.640 Å
晶胞边长 c length_c	26.090 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	99.75 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.1780
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/lr/1lra/1lra.fit
pddf	/app/data/pr_computation/lr/1lra/1lra.pr.out
profile	/app/data/saxs_computation/lr/1lra/1lra.dat