3c2w

Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state

Method: X-RAY DIFFRACTION

▼

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

Bacteriophytochrome

Pseudomonas aeruginosa

当前结构中的状态

Assembly	物理组成	蛋白状态	分子拷贝数	共同组分	数据核对
1	蛋白同源多聚体	同源多聚体	蛋白 2	BILIVERDINE IX ALPHA × 2 water × 2	与蛋白数一致
2	蛋白同源多聚体	同源多聚体	蛋白 2	BILIVERDINE IX ALPHA × 2 water × 2	与蛋白数一致
3	蛋白同源多聚体	同源多聚体	蛋白 2	BILIVERDINE IX ALPHA × 2 water × 2	与蛋白数一致
4	蛋白同源多聚体	同源多聚体	蛋白 2	BILIVERDINE IX ALPHA × 2 water × 2	与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据

UniProt名称	BPHY_PSEAE
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–497； UniProt 1–497 作者链 B； PDB构建体 1–497； UniProt 1–497 作者链 C； PDB构建体 1–497； UniProt 1–497 作者链 D； PDB构建体 1–497； UniProt 1–497 作者链 E； PDB构建体 1–497； UniProt 1–497 作者链 F； PDB构建体 1–497； UniProt 1–497 作者链 G； PDB构建体 1–497； UniProt 1–497 作者链 H； PDB构建体 1–497； UniProt 1–497

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。

▼

2. 结构基本信息 2. Structure Basics

条目编号 entry_id	3c2w
沉积日期 deposition_date	2008-01-25
结构标题 title	Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state
关键词 keywords	;Knot structure, Chromophore, Kinase, Phosphoprotein, Photoreceptor protein, Receptor, Sensory transduction, Transferase, SIGNALING PROTEIN ;; SIGNALING PROTEIN
实验方法 method	X-RAY DIFFRACTION

▼

3. Official assembly/model 理论 SAXS Official SAXS Profiles

页面只读取最新 assembly 计算结果。每一条曲线都对应明确的 PDB、official biological assembly 和 coordinate model。

3c2w__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

3c2w__assembly_2__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

3c2w__assembly_2__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	34.67 Å
Rg（电子密度）	33.84 Å
总 Rg	34.35 Å
原子数	7686
残基数	960
排除体积	135860 Å³
最大 q	0.500 Å⁻¹

Assembly	Model	结构单元	聚集说明	状态	CRYSOL	操作
1	1	`3c2w__assembly_1__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`3c2w__assembly_2__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
3	1	`3c2w__assembly_3__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
4	1	`3c2w__assembly_4__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

描述 description	Bacteriophytochrome
分子量 formula_weight	56823.2 kDa
EC 编号 ec_number	2.7.13.3
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	30494

MTSITPVTLANCEDEPIHVPGAIQPHGALVTLRADGMVLAASENIQALLGFVASPGSYLTQEQVGPEVLRMLEEGLTGNGPWSNSVETRIGEHLFDVIGHSYKEVFYLEFEIRTADTLSITSFTLNAQRIIAQVQLHNDTASLLSNVTDELRRMTGYDRVMAYRFRHDDSGEVVAESRREDLESYLGQRYPASDIPAQARRLYIQNPIRLIADVAYTPMRVFPALNPETNESFDLSYSVLRSVSPIHCEYLTNMGVRASMSISIVVGGKLWGLFSCHHMSPKLIPYPVRMSFQIFSQVCSAIVERLEQGRIAELLRVSTERRLALARRARDADDLFGALAHPDDGIAALIPCDGALVMLGGRTLSIRGDFERQAGNVLQRLQRDPERDIYHTDNWPQPSEDSPDGGDCCGVLAIRFHRQESGWIFWFRHEEVHRIRWGGKPEKLLTIGPSGPRLTPRGSFEAWEEVVRGHSTPWSETDLAIAEKLRLDLMELCLNHALEHHHHHH

来源 Source

来源生物 organism	Pseudomonas aeruginosa
NCBI 分类编号 ncbi_taxonomy_id	287
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	BILIVERDINE IX ALPHA
分子量 formula_weight	582.6 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	30

▼

6. 折叠分类 (SCOP + CATH) 49 domains

SCOP 2.08 (25 domains)

结构域编号 domain_id	d3c2wa1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.1 — GAF domain

结构域编号 domain_id	d3c2wa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.4 — Phytochrome-specific domain

结构域编号 domain_id	d3c2wa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
家族 Family family	d.110.3.9 — BphP N-terminal domain-like

结构域编号 domain_id	d3c2wb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.1 — GAF domain

结构域编号 domain_id	d3c2wb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.4 — Phytochrome-specific domain

结构域编号 domain_id	d3c2wb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
家族 Family family	d.110.3.9 — BphP N-terminal domain-like

结构域编号 domain_id	d3c2wc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.1 — GAF domain

结构域编号 domain_id	d3c2wc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.4 — Phytochrome-specific domain

结构域编号 domain_id	d3c2wc3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
家族 Family family	d.110.3.9 — BphP N-terminal domain-like

结构域编号 domain_id	d3c2wd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.1 — GAF domain

结构域编号 domain_id	d3c2wd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.4 — Phytochrome-specific domain

结构域编号 domain_id	d3c2wd3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
家族 Family family	d.110.3.9 — BphP N-terminal domain-like

结构域编号 domain_id	d3c2we1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.1 — GAF domain

结构域编号 domain_id	d3c2we2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.4 — Phytochrome-specific domain

结构域编号 domain_id	d3c2we3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
家族 Family family	d.110.3.9 — BphP N-terminal domain-like

结构域编号 domain_id	d3c2wf1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.1 — GAF domain

结构域编号 domain_id	d3c2wf2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.4 — Phytochrome-specific domain

结构域编号 domain_id	d3c2wf3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
家族 Family family	d.110.3.9 — BphP N-terminal domain-like

结构域编号 domain_id	d3c2wf4
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d3c2wg1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.1 — GAF domain

结构域编号 domain_id	d3c2wg2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.4 — Phytochrome-specific domain

结构域编号 domain_id	d3c2wg3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
家族 Family family	d.110.3.9 — BphP N-terminal domain-like

结构域编号 domain_id	d3c2wh1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.1 — GAF domain

结构域编号 domain_id	d3c2wh2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.2 — GAF domain-like
家族 Family family	d.110.2.4 — Phytochrome-specific domain

结构域编号 domain_id	d3c2wh3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
家族 Family family	d.110.3.9 — BphP N-terminal domain-like

CATH v4.4 (24 domains)

结构域编号 domain_id	3c2wA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	40 — GAF domain

结构域编号 domain_id	3c2wA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	3c2wA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	270 — PHY domain

结构域编号 domain_id	3c2wB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	40 — GAF domain

结构域编号 domain_id	3c2wB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	3c2wB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	270 — PHY domain

结构域编号 domain_id	3c2wC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	40 — GAF domain

结构域编号 domain_id	3c2wC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	3c2wC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	270 — PHY domain

结构域编号 domain_id	3c2wD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	40 — GAF domain

结构域编号 domain_id	3c2wD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	3c2wD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	270 — PHY domain

结构域编号 domain_id	3c2wE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	40 — GAF domain

结构域编号 domain_id	3c2wE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	3c2wE03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	270 — PHY domain

结构域编号 domain_id	3c2wF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	40 — GAF domain

结构域编号 domain_id	3c2wF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	3c2wF03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	270 — PHY domain

结构域编号 domain_id	3c2wG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	40 — GAF domain

结构域编号 domain_id	3c2wG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	3c2wG03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	270 — PHY domain

结构域编号 domain_id	3c2wH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	40 — GAF domain

结构域编号 domain_id	3c2wH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	3c2wH03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	270 — PHY domain

▶

晶胞边长 a length_a	154.417 Å
晶胞边长 b length_b	164.255 Å
晶胞边长 c length_c	434.868 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	64

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	2.900 Å
最低分辨率 resolution_low	14.996 Å
R 因子 r_factor	0.2221
R_work r_work	0.2188
R_free r_free	0.2832

Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state

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

Bacteriophytochrome

当前结构中的状态

数据库中的同蛋白其他状态

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

3c2w__assembly_2__model_1

3c2w__assembly_2__model_1 | I(q)

3c2w__assembly_2__model_1 | P(r) · Pending

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. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

实体 3 Entity 3 water

6. 折叠分类 (SCOP + CATH) 49 domains

SCOP 2.08 (25 domains)

CATH v4.4 (24 domains)

7. 引用文献 (1)

Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state

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

Bacteriophytochrome

当前结构中的状态

数据库中的同蛋白其他状态

单体

同源二聚体

同源四聚体

其他同源多聚体

异源或核酸复合物

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

3c2w__assembly_2__model_1

3c2w__assembly_2__model_1 | I(q)

3c2w__assembly_2__model_1 | P(r) · Pending

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. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

实体 3 Entity 3 water

6. 折叠分类 (SCOP + CATH) 49 domains

SCOP 2.08 (25 domains)

CATH v4.4 (24 domains)

7. 引用文献 (1)