1g98

CRYSTAL STRUCTURE ANALYSIS OF RABBIT PHOSPHOGLUCOSE ISOMERASE COMPLEXED WITH 5-PHOSPHOARABINONATE, A TRANSITION STATE ANALOGUE

Method: X-RAY DIFFRACTION D_max: 85.1 Å Quality: EXCELLENT

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	1g98
沉积日期 deposition_date	2000-11-22
结构标题 title	CRYSTAL STRUCTURE ANALYSIS OF RABBIT PHOSPHOGLUCOSE ISOMERASE COMPLEXED WITH 5-PHOSPHOARABINONATE, A TRANSITION STATE ANALOGUE
关键词 keywords	Phosphoglucose Isomerase, 5-phosphoarabinonate, transition state analogue, 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	29.84 Å
回转半径 Rg (电子) rg_electron	28.52 Å
零角强度 I(0) i0	243018000.00
分子量 molecular_weight	125090.0 kDa
排除体积 excluded_volume	156920 Å³
包络体积 envelope_volume	180420 Å³
水化壳体积 shell_volume	49082 Å³
包络直径 envelope_diameter	92.2 Å
壳层 Rg shell_rg	38.39 Å
包络 Rg envelope_rg	28.67 Å
形状 Rg shape_rg	28.50 Å
总 Rg total_rg	29.44 Å
总原子数 total_atoms	8820
残基数 n_residues	1110
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	85.1 Å
Rg (实空间) rg_real	29.60 Å
Rg 误差 (实空间) rg_real_error	0.33 Å
I(0) (实空间) i0_real	2.4300e+08
I(0) 误差 (实空间) i0_real_error	3.4170e+06
Rg (倒空间) rg_reciprocal	29.71 Å
I(0) (倒空间) i0_reciprocal	243000000.0000
解质量估计 total_estimate	0.9060
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	40.1 Å
偏度 Skewness skewness	0.038
峰度 Kurtosis kurtosis	-0.546
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	65950000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.900

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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	PHOSPHOGLUCOSE ISOMERASE
分子量 formula_weight	62827.6 kDa
EC 编号 ec_number	5.3.1.9
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	9712

MAALTRNPQFQKLQQWHREHGSELNLRHLFDTDKERFNHFSLTLNTNHGHILLDYSKNLVTEEVMHMLLDLAKSRGVEAARESMFNGEKINSTEDRAVLHVALRNRSNTPIVVDGKDVMPEVNKVLDKMKAFCQRVRSGDWKGYTGKTITDVINIGIGGSDLGPLMVTEALKPYSSGGPRVWFVSNIDGTHIAKTLACLNPESSLFIIASKTFTTQETITNAKTAKDWFLLSAKDPSTVAKHFVALSTNTAKVKEFGIDPQNMFEFWDWVGGRYSLWSAIGLSIALHVGFDNFEQLLSGAHWMDQHFRTTPLEKNAPVLLAMLGIWYINCFGCETQAVLPYDQYLHRFAAYFQQGDMESNGKYITKSGARVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRKGLHHKILLANFLAQTEALMKGKSTEEARKELQAAGKSPEDLMKLLPHKVFEGNRPTNSIVFTKLTPFILGALIAMYEHKIFVQGVVWDINSFDQWGVELGKQLAKKIEPELDGSSPVTSHDSSTNGLINFIKQQREAKIQ

Entity 2 non-polymer

描述 description	5-PHOSPHOARABINONIC ACID
分子量 formula_weight	246.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	892

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1g98a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.80 — SIS domain
超家族 Superfamily superfamily	c.80.1 — SIS domain
家族 Family family	c.80.1.2 — Phosphoglucose isomerase, PGI

结构域编号 domain_id	d1g98b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.80 — SIS domain
超家族 Superfamily superfamily	c.80.1 — SIS domain
家族 Family family	c.80.1.2 — Phosphoglucose isomerase, PGI

CATH v4.4 (6 domains)

结构域编号 domain_id	1g98A01
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1g98A02
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1g98A03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1390 — Phosphoglucose isomerase, C-terminal domain
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1g98B01
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1g98B02
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1g98B03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1390 — Phosphoglucose isomerase, C-terminal domain
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	82.829 Å
晶胞边长 b length_b	116.554 Å
晶胞边长 c length_c	271.824 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	16

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	—
R_work r_work	0.2110
R_free r_free	0.2360

fit	/app/data/saxs_computation/g9/1g98/1g98.fit
pddf	/app/data/pr_computation/g9/1g98/1g98.pr.out
profile	/app/data/saxs_computation/g9/1g98/1g98.dat

CRYSTAL STRUCTURE ANALYSIS OF RABBIT PHOSPHOGLUCOSE ISOMERASE COMPLEXED WITH 5-PHOSPHOARABINONATE, A TRANSITION STATE ANALOGUE

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