1ygy

Crystal Structure of D-3-Phosphoglycerate dehydrogenase From Mycobacterium tuberculosis

Method: X-RAY DIFFRACTION D_max: 112.9 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	1ygy
沉积日期 deposition_date	2005-01-05
结构标题 title	Crystal Structure of D-3-Phosphoglycerate dehydrogenase From Mycobacterium tuberculosis
关键词 keywords	;Oxidoreductase, Phosphoglycerate dehydrogenase, serine biosynthesis, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC ;; OXIDOREDUCTASE
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	36.13 Å
回转半径 Rg (电子) rg_electron	35.55 Å
零角强度 I(0) i0	180289000.00
分子量 molecular_weight	109220.0 kDa
排除体积 excluded_volume	137510 Å³
包络体积 envelope_volume	185100 Å³
水化壳体积 shell_volume	43837 Å³
包络直径 envelope_diameter	114.6 Å
壳层 Rg shell_rg	41.44 Å
包络 Rg envelope_rg	35.23 Å
形状 Rg shape_rg	35.55 Å
总 Rg total_rg	36.01 Å
总原子数 total_atoms	7702
残基数 n_residues	1054
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	112.9 Å
Rg (实空间) rg_real	36.10 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	1.8030e+08
I(0) 误差 (实空间) i0_real_error	3.1590e+06
Rg (倒空间) rg_reciprocal	36.12 Å
I(0) (倒空间) i0_reciprocal	180300000.0000
解质量估计 total_estimate	0.8947
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	41.1 Å
偏度 Skewness skewness	0.234
峰度 Kurtosis kurtosis	-0.675
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	30930000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.750

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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	D-3-phosphoglycerate dehydrogenase
分子量 formula_weight	54705.1 kDa
EC 编号 ec_number	1.1.1.95
来源方法 src_method	man
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	8017

MVSLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS

来源 Source

来源生物 organism	Mycobacterium tuberculosis
NCBI 分类编号 ncbi_taxonomy_id	1773
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	L(+)-TARTARIC ACID
分子量 formula_weight	150.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	315

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1ygya1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.4 — Formate/glycerate dehydrogenases, NAD-domain

结构域编号 domain_id	d1ygya2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.12 — Formate/glycerate dehydrogenase catalytic domain-like
家族 Family family	c.23.12.1 — Formate/glycerate dehydrogenases, substrate-binding domain

结构域编号 domain_id	d1ygya3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.18 — ACT-like
家族 Family family	d.58.18.1 — Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain

结构域编号 domain_id	d1ygya4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.2 — Serine metabolism enzymes domain
家族 Family family	d.81.2.2 — SerA intervening domain-like

结构域编号 domain_id	d1ygyb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.4 — Formate/glycerate dehydrogenases, NAD-domain

结构域编号 domain_id	d1ygyb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.12 — Formate/glycerate dehydrogenase catalytic domain-like
家族 Family family	c.23.12.1 — Formate/glycerate dehydrogenases, substrate-binding domain

结构域编号 domain_id	d1ygyb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.18 — ACT-like
家族 Family family	d.58.18.1 — Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain

结构域编号 domain_id	d1ygyb4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.2 — Serine metabolism enzymes domain
家族 Family family	d.81.2.2 — SerA intervening domain-like

CATH v4.4 (8 domains)

结构域编号 domain_id	1ygyA01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1ygyA02
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1ygyA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	90 — D-3-phosphoglycerate dehydrogenase; domain 3

结构域编号 domain_id	1ygyA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	260 — ACT domain

结构域编号 domain_id	1ygyB01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1ygyB02
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1ygyB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	90 — D-3-phosphoglycerate dehydrogenase; domain 3

结构域编号 domain_id	1ygyB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	260 — ACT domain

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7. 引用文献 (2)

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晶胞边长 a length_a	165.513 Å
晶胞边长 b length_b	165.513 Å
晶胞边长 c length_c	218.144 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	24

空间群 space_group	P 65 2 2
空间群编号 int_tables_number	179
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	48.800 Å
R 因子 r_factor	0.2072
R_work r_work	0.2050
R_free r_free	0.2485

fit	/app/data/saxs_computation/yg/1ygy/1ygy.fit
pddf	/app/data/pr_computation/yg/1ygy/1ygy.pr.out
profile	/app/data/saxs_computation/yg/1ygy/1ygy.dat