1wqa

Crystal Structure of Pyrococcus horikoshii phosphomannomutase/phosphoglucomutase complexed with Mg2+

Method: X-RAY DIFFRACTION D_max: 163.7 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	1wqa
沉积日期 deposition_date	2004-09-24
结构标题 title	Crystal Structure of Pyrococcus horikoshii phosphomannomutase/phosphoglucomutase complexed with Mg2+
关键词 keywords	alpha-beta protein, unphosphorylated form, enzyme-metal complex, ISOMERASE; ISOMERASE
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	48.38 Å
回转半径 Rg (电子) rg_electron	48.67 Å
零角强度 I(0) i0	552928000.00
分子量 molecular_weight	199560.0 kDa
排除体积 excluded_volume	252290 Å³
包络体积 envelope_volume	349540 Å³
水化壳体积 shell_volume	62449 Å³
包络直径 envelope_diameter	170.2 Å
壳层 Rg shell_rg	49.24 Å
包络 Rg envelope_rg	48.02 Å
形状 Rg shape_rg	48.65 Å
总 Rg total_rg	48.73 Å
总原子数 total_atoms	14052
残基数 n_residues	1820
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	163.7 Å
Rg (实空间) rg_real	48.75 Å
Rg 误差 (实空间) rg_real_error	1.69 Å
I(0) (实空间) i0_real	5.5290e+08
I(0) 误差 (实空间) i0_real_error	1.0830e+07
Rg (倒空间) rg_reciprocal	48.39 Å
I(0) (倒空间) i0_reciprocal	552700000.0000
解质量估计 total_estimate	0.8346
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	49.6 Å
偏度 Skewness skewness	0.440
峰度 Kurtosis kurtosis	-0.384
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	34220000.0000
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: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.278

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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 (3)

Entity 1 polymer

描述 description	phospho-sugar mutase
分子量 formula_weight	49938.3 kDa
EC 编号 ec_number	5.4.2.8
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	14766

MGKLFGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKEREAIVEELFFKEDFDRAKWYEIGEVRREDIIKPYIEAIKSKVDVEAIKKRKPFVVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKGGGLLVTTVATSNLLDDIAKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKKFSELIDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKIIFEDGWVLVRASGTEPIIRIFSEAKSKEKAQEYLNLGIELLEKALS

来源 Source

来源生物 organism	Pyrococcus horikoshii
NCBI 分类编号 ncbi_taxonomy_id	53953
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 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	714

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6. 折叠分类 (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

结构域编号 domain_id	1wqaA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1wqaA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1wqaA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1wqaA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	50 — Alpha-D-phosphohexomutase, C-terminal domain

结构域编号 domain_id	1wqaB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1wqaB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1wqaB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1wqaB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	50 — Alpha-D-phosphohexomutase, C-terminal domain

结构域编号 domain_id	1wqaC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1wqaC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1wqaC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1wqaC04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	50 — Alpha-D-phosphohexomutase, C-terminal domain

结构域编号 domain_id	1wqaD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1wqaD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1wqaD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1wqaD04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	50 — Alpha-D-phosphohexomutase, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	77.653 Å
晶胞边长 b length_b	137.916 Å
晶胞边长 c length_c	98.409 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	93.27 °
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	2.000 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	—
R_work r_work	0.2162
R_free r_free	0.2359

fit	/app/data/saxs_computation/wq/1wqa/1wqa.fit
pddf	/app/data/pr_computation/wq/1wqa/1wqa.pr.out
profile	/app/data/saxs_computation/wq/1wqa/1wqa.dat

Crystal Structure of Pyrococcus horikoshii phosphomannomutase/phosphoglucomutase complexed with Mg2+

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