9m5w

;Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 343K 1.58 angstrom ;

Method: X-RAY DIFFRACTION D_max: 61.6 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	9m5w
沉积日期 deposition_date	2025-03-06
最后修订 last_revision	2026-03-11
结构标题 title	;Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 343K 1.58 angstrom ;
关键词 keywords	MTAP, complex, phosphorylase, 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	18.96 Å
回转半径 Rg (电子) rg_electron	17.87 Å
零角强度 I(0) i0	17231400.00
分子量 molecular_weight	30955.0 kDa
排除体积 excluded_volume	38557 Å³
包络体积 envelope_volume	43620 Å³
水化壳体积 shell_volume	19937 Å³
包络直径 envelope_diameter	59.5 Å
壳层 Rg shell_rg	24.67 Å
包络 Rg envelope_rg	18.22 Å
形状 Rg shape_rg	17.88 Å
总 Rg total_rg	18.79 Å
总原子数 total_atoms	2174
残基数 n_residues	273
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	61.6 Å
Rg (实空间) rg_real	18.83 Å
Rg 误差 (实空间) rg_real_error	0.40 Å
I(0) (实空间) i0_real	1.7230e+07
I(0) 误差 (实空间) i0_real_error	2.1700e+05
Rg (倒空间) rg_reciprocal	18.85 Å
I(0) (倒空间) i0_reciprocal	17230000.0000
解质量估计 total_estimate	0.8015
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	24.8 Å
偏度 Skewness skewness	0.140
峰度 Kurtosis kurtosis	-0.380
角度范围 angular_range	— – 0.4200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5234000.0000
实空间数据点数 n_real_points	73
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.811; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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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 (5)

Entity 1 polymer

描述 description	;S-methyl-5'-thioadenosine phosphorylase ;
分子量 formula_weight	30777.3 kDa
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	2236

MFEITRPPGVRAHVGVIGGSGLYDPGIVENPVEVKVSTPYGNPSDFIVVGDVAGVKVAFLPRHGRGHRIPPHAINYRANIWALKALGVKWVISVSAVGSLREDYRPGDFVVPDQFIDMTKNRRHYTFYDGPVTVHVSMADPFCEDLRQRLIDSGRRLGYTVHERGTYVCIEGPRFSTRAESRVWKDVFKADIIGMTLVPEINLACEAQLCYATLAMVTDYDVWADRPVTAEEVERVMISNVERARRMLYDVIPKLAGEPELERCSCCRALDTAAI

来源 Source

来源生物 organism	Aeropyrum pernix K1
NCBI 分类编号 ncbi_taxonomy_id	272557
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	5'-DEOXY-5'-METHYLTHIOADENOSINE
分子量 formula_weight	297.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	48

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7. 引用文献 (1)

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晶胞边长 a length_a	78.940 Å
晶胞边长 b length_b	78.940 Å
晶胞边长 c length_c	233.481 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	120.00 °
晶胞分子数 Z z_pdb	18

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	1.580 Å
最低分辨率 resolution_low	44.390 Å
R 因子 r_factor	—
R_work r_work	0.1412
R_free r_free	0.1628

fit	/app/data/saxs_computation/m5/9m5w/9m5w.fit
pddf	/app/data/pr_computation/m5/9m5w/9m5w.pr.out
profile	/app/data/saxs_computation/m5/9m5w/9m5w.dat

;Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 343K 1.58 angstrom ;

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