1c7o

CRYSTAL STRUCTURE OF CYSTALYSIN FROM TREPONEMA DENTICOLA CONTAINS A PYRIDOXAL 5'-PHOSPHATE-L-AMINOETHOXYVINYLGLYCINE COMPLEX

Method: X-RAY DIFFRACTION D_max: 199.8 Å Quality: GOOD

▼

1. 蛋白身份与相关结构 Protein Identity & Related Structures

CYSTALYSIN

Treponema denticola

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白同源多聚体同源多聚体蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 A； UniProt 1–399 链 B； UniProt 1–399	未记录	PPG (2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, MES, pH 6.5, VAPOR DIFFUSION/SITTING DROP, temperature 293.0K	分辨率 2.50 Å R-free 0.260
2	蛋白同源多聚体同源多聚体蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 C； UniProt 1–399 链 D； UniProt 1–399	未记录	PPG (2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, MES, pH 6.5, VAPOR DIFFUSION/SITTING DROP, temperature 293.0K	分辨率 2.50 Å R-free 0.260
3	蛋白同源多聚体同源多聚体蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 E； UniProt 1–399 链 F； UniProt 1–399	未记录	PPG (2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, MES, pH 6.5, VAPOR DIFFUSION/SITTING DROP, temperature 293.0K	分辨率 2.50 Å R-free 0.260
4	蛋白同源多聚体同源多聚体蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 G； UniProt 1–399 链 H； UniProt 1–399	未记录	PPG (2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, MES, pH 6.5, VAPOR DIFFUSION/SITTING DROP, temperature 293.0K	分辨率 2.50 Å R-free 0.260

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 1C7O	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1C7N CRYSTAL STRUCTURE OF CYSTALYSIN FROM TREPONEMA DENTICOLA CONTAINS A PYRIDOXAL 5'-PHOSPHATE COFACTOR 提交 2000-03-16	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 1–399（399 aa）链 B 1–399（399 aa）	未记录	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, MES, pH 6.5, vapor diffusion/sitting drop, temperature 293.0K	分辨率 1.90 Å R-free 0.247
1C7N CRYSTAL STRUCTURE OF CYSTALYSIN FROM TREPONEMA DENTICOLA CONTAINS A PYRIDOXAL 5'-PHOSPHATE COFACTOR 提交 2000-03-16	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 C 1–399（399 aa）链 D 1–399（399 aa）	未记录	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, MES, pH 6.5, vapor diffusion/sitting drop, temperature 293.0K	分辨率 1.90 Å R-free 0.247
1C7N CRYSTAL STRUCTURE OF CYSTALYSIN FROM TREPONEMA DENTICOLA CONTAINS A PYRIDOXAL 5'-PHOSPHATE COFACTOR 提交 2000-03-16	配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 E 1–399（399 aa）链 F 1–399（399 aa）	未记录	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, MES, pH 6.5, vapor diffusion/sitting drop, temperature 293.0K	分辨率 1.90 Å R-free 0.247
1C7N CRYSTAL STRUCTURE OF CYSTALYSIN FROM TREPONEMA DENTICOLA CONTAINS A PYRIDOXAL 5'-PHOSPHATE COFACTOR 提交 2000-03-16	配体/离子不同实验环境不同结构质量不同	Assembly 4 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 G 1–399（399 aa）链 H 1–399（399 aa）	未记录	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, MES, pH 6.5, vapor diffusion/sitting drop, temperature 293.0K	分辨率 1.90 Å R-free 0.247

共 1 个其他 PDB 条目、4 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	Q56257_TREDE
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–399； UniProt 1–399 作者链 B； PDB构建体 1–399； UniProt 1–399 作者链 C； PDB构建体 1–399； UniProt 1–399 作者链 D； PDB构建体 1–399； UniProt 1–399 作者链 E； PDB构建体 1–399； UniProt 1–399 作者链 F； PDB构建体 1–399； UniProt 1–399 作者链 G； PDB构建体 1–399； UniProt 1–399 作者链 H； PDB构建体 1–399； UniProt 1–399

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

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

▼

2. 结构基本信息 2. Structure Basics

条目编号 entry_id	1c7o
沉积日期 deposition_date	2000-03-16
结构标题 title	CRYSTAL STRUCTURE OF CYSTALYSIN FROM TREPONEMA DENTICOLA CONTAINS A PYRIDOXAL 5'-PHOSPHATE-L-AMINOETHOXYVINYLGLYCINE COMPLEX
关键词 keywords	Transferase, Aminotransferase; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

▼

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	66.49 Å
回转半径 Rg (电子) rg_electron	67.20 Å
零角强度 I(0) i0	1742980000.00
分子量 molecular_weight	367470.0 kDa
排除体积 excluded_volume	465780 Å³
包络体积 envelope_volume	672510 Å³
水化壳体积 shell_volume	87217 Å³
包络直径 envelope_diameter	223.3 Å
壳层 Rg shell_rg	62.59 Å
包络 Rg envelope_rg	64.26 Å
形状 Rg shape_rg	67.19 Å
总 Rg total_rg	67.13 Å
总原子数 total_atoms	25864
残基数 n_residues	3152
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

▼

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	199.8 Å
Rg (实空间) rg_real	67.04 Å
Rg 误差 (实空间) rg_real_error	1.80 Å
I(0) (实空间) i0_real	1.7430e+09
I(0) 误差 (实空间) i0_real_error	3.5490e+07
Rg (倒空间) rg_reciprocal	65.90 Å
I(0) (倒空间) i0_reciprocal	1739000000.0000
解质量估计 total_estimate	0.8219
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	74.9 Å
偏度 Skewness skewness	0.311
峰度 Kurtosis kurtosis	-0.800
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	44110000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.879; Smooth: 0.000

▶

5. 晶体学与实验 5. Crystallography & Experiment

▶

6. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

描述 description	CYSTALYSIN
分子量 formula_weight	46278.4 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	27138

MIYDFTTKISRKNLGSLKWDLMYSQNPEVGNEVVPLSVADMEFKNPPELIEGLKKYLDETVLGYTGPTEEYKKTVKKWMKDRHQWDIQTDWIINTAGVVPAVFNAVREFTKPGDGVIIITPVYYPFFMAIKNQERKIIECELLEKDGYYTIDFQKLEKLSKDKNNKALLFCSPHNPVGRVWKKDELQKIKDIVLKSDLMLWSDEIHFDLIMPGYEHTVFQSIDEQLADKTITFTAPSKTFNIAGMGMSNIIIKNPDIRERFTKSRDATSGMPFTTLGYKACEICYKECGKWLDGCIKVIDKNQRIVKDFFEVNHPEIKAPLIEGTYLQWIDFRALKMDHKAMEEFMIHKAQIFFDEGYIFGDGGIGFERINLAAPSSVIQESLERLNKALKDLKNRHLK

来源 Source

来源生物 organism	Treponema denticola
NCBI 分类编号 ncbi_taxonomy_id	158
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	(2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid
分子量 formula_weight	389.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

实体 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	1274

▼

7. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1c7oa_
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.67.1.3 — Cystathionine synthase-like

结构域编号 domain_id	d1c7ob_
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.67.1.3 — Cystathionine synthase-like

结构域编号 domain_id	d1c7oc_
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.67.1.3 — Cystathionine synthase-like

结构域编号 domain_id	d1c7od_
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.67.1.3 — Cystathionine synthase-like

结构域编号 domain_id	d1c7oe_
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.67.1.3 — Cystathionine synthase-like

结构域编号 domain_id	d1c7of_
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.67.1.3 — Cystathionine synthase-like

结构域编号 domain_id	d1c7og_
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.67.1.3 — Cystathionine synthase-like

结构域编号 domain_id	d1c7oh_
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.67.1.3 — Cystathionine synthase-like

CATH v4.4 (16 domains)

结构域编号 domain_id	1c7oA01
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	1c7oA02
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	1c7oB01
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	1c7oB02
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	1c7oC01
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	1c7oC02
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	1c7oD01
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	1c7oD02
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	1c7oE01
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	1c7oE02
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	1c7oF01
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	1c7oF02
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	1c7oG01
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	1c7oG02
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	1c7oH01
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	1c7oH02
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)

▶

8. 引用文献 (1)

▶

晶胞边长 a length_a	89.373 Å
晶胞边长 b length_b	107.929 Å
晶胞边长 c length_c	176.156 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.17 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	2.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2010
R_work r_work	0.1930
R_free r_free	0.2600

fit	/app/data/saxs_computation/c7/1c7o/1c7o.fit
pddf	/app/data/pr_computation/c7/1c7o/1c7o.pr.out
profile	/app/data/saxs_computation/c7/1c7o/1c7o.dat