1wyu

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form

Method: X-RAY DIFFRACTION D_max: 170.1 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	1wyu
沉积日期 deposition_date	2005-02-17
结构标题 title	Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form
关键词 keywords	ALPHA(2)BETA(2) TETRAMER, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, OXIDOREDUCTASE; 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	50.00 Å
回转半径 Rg (电子) rg_electron	49.87 Å
零角强度 I(0) i0	2145600000.00
分子量 molecular_weight	399300.0 kDa
排除体积 excluded_volume	504710 Å³
包络体积 envelope_volume	613980 Å³
水化壳体积 shell_volume	99802 Å³
包络直径 envelope_diameter	175.3 Å
壳层 Rg shell_rg	55.45 Å
包络 Rg envelope_rg	49.43 Å
形状 Rg shape_rg	49.87 Å
总 Rg total_rg	50.03 Å
总原子数 total_atoms	28192
残基数 n_residues	3640
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	170.1 Å
Rg (实空间) rg_real	50.06 Å
Rg 误差 (实空间) rg_real_error	1.47 Å
I(0) (实空间) i0_real	2.1460e+09
I(0) 误差 (实空间) i0_real_error	4.0590e+07
Rg (倒空间) rg_reciprocal	50.00 Å
I(0) (倒空间) i0_reciprocal	2145000000.0000
解质量估计 total_estimate	0.8650
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	54.9 Å
偏度 Skewness skewness	0.383
峰度 Kurtosis kurtosis	-0.320
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	386700000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.734

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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 (4)

Entity 1 polymer

描述 description	glycine dehydrogenase (decarboxylating) subunit 1
分子量 formula_weight	47168.1 kDa
EC 编号 ec_number	1.4.4.2
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,C,E,G
原子数 atom_count	30337

MDYTPHTEEEIREMLRRVGAASLEDLFAHLPKEILSPPIDLPEPLPEWKVLEELRRLAAQNLPAHKAFLGGGVRSHHVPPVVQALAARGEFLTAYTPYQPEVSQGVLQATFEYQTMIAELAGLEIANASMYDGATALAEGVLLALRETGRMGVLVSQGVHPEYRAVLRAYLEAVGAKLLTLPLEGGRTPLPEVGEEVGAVVVQNPNFLGALEDLGPFAEAAHGAGALFVAVADPLSLGVLKPPGAYGADIAVGDGQSLGLPMGFGGPHFGFLATKKAFVRQLPGRLVSETVDVEGRRGFILTLQAREQYIRRAKAKSNITTNAQLTALMGAMYLAALGPEGLREVALKSVEMAHKLHALLLEVPGVRPFTPKPFFNEFALALPKDPEAVRRALAERGFHGATPVPREYGENLALFAATELHEEEDLLALREALKEVLA

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	300852
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	glycine dehydrogenase subunit 2 (P-protein)
分子量 formula_weight	52784.7 kDa
EC 编号 ec_number	1.4.4.2
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	B,D,F,H

MSFPLIFERSRKGRRGLKLVKAVPKAEDLIPKEHLREVPPRLPEVDELTLVRHYTGLSRRQVGVDTTFYPLGSCTMKYNPKLHEEAARLFADLHPYQDPRTAQGALRLMWELGEYLKALTGMDAITLEPAAGAHGELTGILIIRAYHEDRGEGRTRRVVLVPDSAHGSNPATASMAGYQVREIPSGPEGEVDLEALKRELGPHVAALMLTNPNTLGLFERRILEISRLCKEAGVQLYYDGANLNAIMGWARPGDMGFDVVHLNLHKTFTVPHGGGGPGSGPVGVKAHLAPYLPVPLVERGEEGFYLDFDRPKSIGRVRSFYGNFLALVRAWAYIRTLGLEGLKKAAALAVLNARYLKELLKEKGYRVPYDGPSMHEFVAQPPEGFRALDLAKGLLELGFHPPTVYFPLIVKEALMVEPTETEAKETLEAFAEAMGALLKKPKEWLENAPYSTPVRRLDELRANKHPKLTYFDEG

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	300852
宿主生物 host_organism	Escherichia coli

Entity 3 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 4 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	2145

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6. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1wyua_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

结构域编号 domain_id	d1wyub_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

结构域编号 domain_id	d1wyuc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

结构域编号 domain_id	d1wyud_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

结构域编号 domain_id	d1wyue_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

结构域编号 domain_id	d1wyuf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

结构域编号 domain_id	d1wyug_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

结构域编号 domain_id	d1wyuh_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

CATH v4.4 (20 domains)

结构域编号 domain_id	1wyuA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

结构域编号 domain_id	1wyuA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

结构域编号 domain_id	1wyuB01
类 Class class	6 — Special
架构 Architecture architecture	20 — Other non-globular
拓扑 Topology topology	440 — Translocated Intimin Receptor; Chain T
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1wyuB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

结构域编号 domain_id	1wyuB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

结构域编号 domain_id	1wyuC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

结构域编号 domain_id	1wyuC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

结构域编号 domain_id	1wyuD01
类 Class class	6 — Special
架构 Architecture architecture	20 — Other non-globular
拓扑 Topology topology	440 — Translocated Intimin Receptor; Chain T
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1wyuD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

结构域编号 domain_id	1wyuD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

结构域编号 domain_id	1wyuE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

结构域编号 domain_id	1wyuE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

结构域编号 domain_id	1wyuF01
类 Class class	6 — Special
架构 Architecture architecture	20 — Other non-globular
拓扑 Topology topology	440 — Translocated Intimin Receptor; Chain T
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1wyuF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

结构域编号 domain_id	1wyuF03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

结构域编号 domain_id	1wyuG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

结构域编号 domain_id	1wyuG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

结构域编号 domain_id	1wyuH01
类 Class class	6 — Special
架构 Architecture architecture	20 — Other non-globular
拓扑 Topology topology	440 — Translocated Intimin Receptor; Chain T
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1wyuH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

结构域编号 domain_id	1wyuH03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

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7. 引用文献 (1)

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晶胞边长 a length_a	134.874 Å
晶胞边长 b length_b	166.673 Å
晶胞边长 c length_c	189.007 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	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	49.570 Å
R 因子 r_factor	0.1910
R_work r_work	0.1890
R_free r_free	0.2290

fit	/app/data/saxs_computation/wy/1wyu/1wyu.fit
pddf	/app/data/pr_computation/wy/1wyu/1wyu.pr.out
profile	/app/data/saxs_computation/wy/1wyu/1wyu.dat

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form

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

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (8 domains)

CATH v4.4 (20 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)