SAXSdb — 2c4m

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2c4m
沉积日期 deposition_date	2005-10-20
结构标题 title	Starch phosphorylase: structural studies explain oxyanion-dependent kinetic stability and regulatory control.
关键词 keywords	ALLOSTERIC CONTROL, PHOSPHATE DEPENDENCE, STARCH DEGRADING, PHOSPHORYLASE, TRANSFERASE, GLYCOSYLTRANSFERASE; 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	48.08 Å
回转半径 Rg (电子) rg_electron	47.44 Å
零角强度 I(0) i0	1913970000.00
分子量 molecular_weight	361400.0 kDa
排除体积 excluded_volume	449790 Å³
包络体积 envelope_volume	573790 Å³
水化壳体积 shell_volume	96048 Å³
包络直径 envelope_diameter	167.6 Å
壳层 Rg shell_rg	55.91 Å
包络 Rg envelope_rg	46.51 Å
形状 Rg shape_rg	47.42 Å
总 Rg total_rg	47.78 Å
总原子数 total_atoms	25500
残基数 n_residues	3158
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	154.5 Å
Rg (实空间) rg_real	47.84 Å
Rg 误差 (实空间) rg_real_error	1.05 Å
I(0) (实空间) i0_real	1.9140e+09
I(0) 误差 (实空间) i0_real_error	3.5980e+07
Rg (倒空间) rg_reciprocal	48.08 Å
I(0) (倒空间) i0_reciprocal	1915000000.0000
解质量估计 total_estimate	0.8798
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	65.5 Å
偏度 Skewness skewness	0.176
峰度 Kurtosis kurtosis	-0.406
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	316200000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.779

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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	GLYCOGEN PHOSPHORYLASE
分子量 formula_weight	90662.9 kDa
EC 编号 ec_number	2.4.1.1
突变 mutation	YES
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	26654

MSPEKQPLPAALVGSHVRAAAGTPADLATDRKFWTGLSRAVQERIADDWERTREAYGAARQQHYFSAEFLMGRALLNNLTNLGLVDEAAAATRELGHELTDILEIENDAALGNGGLGRLAACFLDSAVTQDYPVTGYGLLYRFGLFRQSFNEGFQVEKPDPWREEEYPFTIRRASDQLVVCFDDMKTRAIPYDMPITGYGTHNVGTLRLWKAEPWEEFDYDAFNAQRFTDAIIERERVSDICRVLYPNDTTYEGKKLRVRQQYFFTSASLQAMIQDHLAHHKDLSNFAEFHSVQLNDTHPVLAIPELMRLLMDEHDMGWEESWAIVSKTFAYTNHTVLTEALEQWDEQIFQQLFWRVWEIIAEIDRRFRLERAADGLDEETINRMAPIQHGTVHMAWIACYAAYSINGVAALHTEIIKAETLADWYALWPEKFNNKTNGVTPRRWLRMINPGLSDLLTRLSGSDDWVTDLDELKKLRSYADDKSVLEELRAIKAANKQDFAEWILERQGIEIDPESIFDVQIKRLHEYKRQLMNALYVLDLYFRIKEDGLTDIPARTVIFGAKAAPGYVRAKAIIKLINSIADLVNNDPEVSPLLKVVFVENYNVSPAEHILPASDVSEQISTAGKEASGTSNMKFMMNGALTLGTMDGANVEIVDSVGEENAYIFGARVEELPALRESYKPYELYETVPGLKRALDALDNGTLNDNNSGLFYDLKHSLIHGYGKDASDTYYVLGDFADYRETRDRMAADYASDPLGWARMAWINICESGRFSSDRTIRDYATEIWKLEPTPAVKK

来源 Source

来源生物 organism	CORYNEBACTERIUM CALLUNAE
NCBI 分类编号 ncbi_taxonomy_id	1721
宿主生物 host_organism	Escherichia coli DH5[alpha]

Entity 2 non-polymer

描述 description	PYRIDOXAL-5'-PHOSPHATE
分子量 formula_weight	247.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 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	9

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	19

Entity 5 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	1154

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	2c4mA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

结构域编号 domain_id	2c4mA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

结构域编号 domain_id	2c4mB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

结构域编号 domain_id	2c4mB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

结构域编号 domain_id	2c4mC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

结构域编号 domain_id	2c4mC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

结构域编号 domain_id	2c4mD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

结构域编号 domain_id	2c4mD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

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7. 引用文献 (1)

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晶胞边长 a length_a	99.266 Å
晶胞边长 b length_b	187.620 Å
晶胞边长 c length_c	129.315 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	112.48 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	30.000 Å
R 因子 r_factor	0.2160
R_work r_work	0.2160
R_free r_free	0.2320

fit	/app/data/saxs_computation/c4/2c4m/2c4m.fit
pddf	/app/data/pr_computation/c4/2c4m/2c4m.pr.out
profile	/app/data/saxs_computation/c4/2c4m/2c4m.dat

Starch phosphorylase: structural studies explain oxyanion-dependent kinetic stability and regulatory control.

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