1dv3

PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-SEPARATED D+QAQB-STATE WITH THE PROTON TRANSFER INHIBITOR CD2+

Method: X-RAY DIFFRACTION Dmax: 150.5 Å Quality: GOOD

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

PHOTOSYNTHETIC REACTION CENTER REACTION CENTER

物种未注明

UniProt P02954

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 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 L; UniProt 1–281 片段:L CHAIN PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02953) PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, heptanetriol, TRIS-HCL, LDAO detergent, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K 分辨率 2.50 Å R-free 0.252
2 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 R; UniProt 1–281 片段:L CHAIN PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02953) PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, heptanetriol, TRIS-HCL, LDAO detergent, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K 分辨率 2.50 Å R-free 0.252

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。

共 39 个其他 PDB 条目、47 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 RCEL_RHOSH
Isoform
PDB实体 1
链与序列区间 作者链 L; PDB构建体 1–281; UniProt 1–281 作者链 R; PDB构建体 1–281; UniProt 1–281

PHOTOSYNTHETIC REACTION CENTER REACTION CENTER

物种未注明

UniProt P02953

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 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 M; UniProt 1–307 片段:M CHAIN PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02954) PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, heptanetriol, TRIS-HCL, LDAO detergent, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K 分辨率 2.50 Å R-free 0.252
2 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 S; UniProt 1–307 片段:M CHAIN PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02954) PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, heptanetriol, TRIS-HCL, LDAO detergent, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K 分辨率 2.50 Å R-free 0.252

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。

共 39 个其他 PDB 条目、47 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 RCEM_RHOSH
Isoform
PDB实体 2
链与序列区间 作者链 M; PDB构建体 1–307; UniProt 1–307 作者链 S; PDB构建体 1–307; UniProt 1–307

PHOTOSYNTHETIC REACTION CENTER REACTION CENTER

物种未注明

UniProt P11846

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 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 H; UniProt 1–260 片段:H CHAIN PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02954) PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02953) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, heptanetriol, TRIS-HCL, LDAO detergent, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K 分辨率 2.50 Å R-free 0.252
2 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 T; UniProt 1–260 片段:H CHAIN PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02954) PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02953) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, heptanetriol, TRIS-HCL, LDAO detergent, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K 分辨率 2.50 Å R-free 0.252

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。

共 39 个其他 PDB 条目、47 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 RCEH_RHOSH
Isoform
PDB实体 3
链与序列区间 作者链 H; PDB构建体 1–260; UniProt 1–260 作者链 T; PDB构建体 1–260; UniProt 1–260

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

SAXS profile for 1dv3

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1dv3
下载 Download

2. 结构基本信息 2. Structure Basics

条目编号 entry_id1dv3
沉积日期 deposition_date2000-01-19
结构标题 titlePHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-SEPARATED D+QAQB-STATE WITH THE PROTON TRANSFER INHIBITOR CD2+
关键词 keywords;Bacterial Photosynthesis, Rhodobacter sphaeroides, Metal Ion Binding, Cation Binding, Proton Transfer, Integral Membrane Protein, PHOTOSYNTHESIS ;; PHOTOSYNTHESIS
实验方法 methodX-RAY DIFFRACTION

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

回转半径 Rg (Guinier) rg_guinier52.27
回转半径 Rg (电子) rg_electron51.66
零角强度 I(0) i0434835000.00
分子量 molecular_weight195390.0 kDa
排除体积 excluded_volume252160 ų
包络体积 envelope_volume338170 ų
水化壳体积 shell_volume54026 ų
包络直径 envelope_diameter163.5
壳层 Rg shell_rg56.42
包络 Rg envelope_rg49.71
形状 Rg shape_rg51.58
总 Rg total_rg52.12
总原子数 total_atoms13865
残基数 n_residues1652
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

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

最大尺寸 Dmax dmax150.5
Rg (实空间) rg_real52.49
Rg 误差 (实空间) rg_real_error1.30
I(0) (实空间) i0_real4.3480e+08
I(0) 误差 (实空间) i0_real_error7.5090e+06
Rg (倒空间) rg_reciprocal52.05
I(0) (倒空间) i0_reciprocal434600000.0000
解质量估计 total_estimate0.7684
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary35.1
偏度 Skewness skewness0.235
峰度 Kurtosis kurtosis-1.048
角度范围 angular_range— – 0.1500 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha21840000.0000
实空间数据点数 n_real_points31
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.654; Smooth: 0.000

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

6. 实体与聚合物信息 Entities & Polymers (11)

7. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

结构域编号 domain_idd1dv3h1
类 Class classb — All beta proteins
折叠类型 Fold foldb.41 — PRC-barrel domain
超家族 Superfamily superfamilyb.41.1 — PRC-barrel domain
家族 Family familyb.41.1.1 — Photosynthetic reaction centre, H-chain, cytoplasmic domain
结构域编号 domain_idd1dv3h2
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.23 — Single transmembrane helix
超家族 Superfamily superfamilyf.23.10 — Photosystem II reaction centre subunit H, transmembrane region
家族 Family familyf.23.10.1 — Photosystem II reaction centre subunit H, transmembrane region
结构域编号 domain_idd1dv3l_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.26 — Bacterial photosystem II reaction centre, L and M subunits
超家族 Superfamily superfamilyf.26.1 — Bacterial photosystem II reaction centre, L and M subunits
家族 Family familyf.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits
结构域编号 domain_idd1dv3m_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.26 — Bacterial photosystem II reaction centre, L and M subunits
超家族 Superfamily superfamilyf.26.1 — Bacterial photosystem II reaction centre, L and M subunits
家族 Family familyf.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits
结构域编号 domain_idd1dv3r_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.26 — Bacterial photosystem II reaction centre, L and M subunits
超家族 Superfamily superfamilyf.26.1 — Bacterial photosystem II reaction centre, L and M subunits
家族 Family familyf.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits
结构域编号 domain_idd1dv3s_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.26 — Bacterial photosystem II reaction centre, L and M subunits
超家族 Superfamily superfamilyf.26.1 — Bacterial photosystem II reaction centre, L and M subunits
家族 Family familyf.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits
结构域编号 domain_idd1dv3t1
类 Class classb — All beta proteins
折叠类型 Fold foldb.41 — PRC-barrel domain
超家族 Superfamily superfamilyb.41.1 — PRC-barrel domain
家族 Family familyb.41.1.1 — Photosynthetic reaction centre, H-chain, cytoplasmic domain
结构域编号 domain_idd1dv3t2
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.23 — Single transmembrane helix
超家族 Superfamily superfamilyf.23.10 — Photosystem II reaction centre subunit H, transmembrane region
家族 Family familyf.23.10.1 — Photosystem II reaction centre subunit H, transmembrane region

CATH v4.4 (12 domains)

结构域编号 domain_id1dv3H01
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology540 — Photosynthetic Reaction Center; Chain H, domain 1
同源超家族 H-superfamily homologous superfamily10 — Photosynthetic reaction centre, H subunit, N-terminal domain
结构域编号 domain_id1dv3H02
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology50 — Photosynthetic Reaction Center; Chain H, domain 2
同源超家族 H-superfamily homologous superfamily10 — Photosynthetic Reaction Center, subunit H, domain 2
结构域编号 domain_id1dv3L01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
同源超家族 H-superfamily homologous superfamily10 — Photosystem II protein D1-like
结构域编号 domain_id1dv3L02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
同源超家族 H-superfamily homologous superfamily10 — Photosystem II protein D1-like
结构域编号 domain_id1dv3M01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
同源超家族 H-superfamily homologous superfamily10 — Photosystem II protein D1-like
结构域编号 domain_id1dv3M02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
同源超家族 H-superfamily homologous superfamily10 — Photosystem II protein D1-like
结构域编号 domain_id1dv3R01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
同源超家族 H-superfamily homologous superfamily10 — Photosystem II protein D1-like
结构域编号 domain_id1dv3R02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
同源超家族 H-superfamily homologous superfamily10 — Photosystem II protein D1-like
结构域编号 domain_id1dv3S01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
同源超家族 H-superfamily homologous superfamily10 — Photosystem II protein D1-like
结构域编号 domain_id1dv3S02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
同源超家族 H-superfamily homologous superfamily10 — Photosystem II protein D1-like
结构域编号 domain_id1dv3T01
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology540 — Photosynthetic Reaction Center; Chain H, domain 1
同源超家族 H-superfamily homologous superfamily10 — Photosynthetic reaction centre, H subunit, N-terminal domain
结构域编号 domain_id1dv3T02
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology50 — Photosynthetic Reaction Center; Chain H, domain 2
同源超家族 H-superfamily homologous superfamily10 — Photosynthetic Reaction Center, subunit H, domain 2

8. 引用文献 (4)

9. 文件与曲线 (10)