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1brw

THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION

Method: X-RAY DIFFRACTION Dmax: 110.8 Å Quality: GOOD
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1. 蛋白身份与相关结构 Protein Identity & Related Structures

PROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE)

物种未注明

UniProt P77836

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 1–433 链 B； UniProt 1–433 未记录 PO4 PHOSPHATE ION × 2 CA CALCIUM ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 URA URACIL × 1 X-RAY DIFFRACTION X-ray结晶条件：pH 6；0.1 M MES PH 6.0-6.2 25% PEG 6000 PSEUDOURIDINE AT 10X PROTEIN CONCENTRATION 分辨率 2.10 Å R-free 0.276

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。

数据库中没有找到同一 UniProt 蛋白的其他 PDB 条目。

查看构建体与数据证据
UniProt名称 PDP_BACST
Isoform —
PDB实体 1
链与序列区间 作者链 A； PDB构建体 1–433； UniProt 1–433 作者链 B； PDB构建体 1–433； UniProt 1–433

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 1brw

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1brw
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id1brw
沉积日期 deposition_date1998-08-25
结构标题 titleTHE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION
关键词 keywordsNUCLEOSIDE PHOSPHORYLASE, DOMAIN MOVEMENT, TRANSFERASE; TRANSFERASE
实验方法 methodX-RAY DIFFRACTION
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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier33.85 Å
回转半径 Rg (电子) rg_electron33.55 Å
零角强度 I(0) i0133171000.00
分子量 molecular_weight92712.0 kDa
排除体积 excluded_volume116470 ų
包络体积 envelope_volume145980 ų
水化壳体积 shell_volume37692 ų
包络直径 envelope_diameter110.9 Å
壳层 Rg shell_rg39.05 Å
包络 Rg envelope_rg33.32 Å
形状 Rg shape_rg33.60 Å
总 Rg total_rg33.80 Å
总原子数 total_atoms6482
残基数 n_residues866
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 Å−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
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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax110.8 Å
Rg (实空间) rg_real34.00 Å
Rg 误差 (实空间) rg_real_error0.86 Å
I(0) (实空间) i0_real1.3320e+08
I(0) 误差 (实空间) i0_real_error2.2170e+06
Rg (倒空间) rg_reciprocal33.91 Å
I(0) (倒空间) i0_reciprocal133200000.0000
解质量估计 total_estimate0.8498
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary30.6 Å
偏度 Skewness skewness0.424
峰度 Kurtosis kurtosis-0.609
角度范围 angular_range— – 0.2350 Å−1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha44820000.0000
实空间数据点数 n_real_points48
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.831; Smooth: 0.837
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5. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (6)

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7. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_idd1brwa1
类 Class classa — All alpha proteins
折叠类型 Fold folda.46 — Methionine synthase domain-like
超家族 Superfamily superfamilya.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
家族 Family familya.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
结构域编号 domain_idd1brwa2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
超家族 Superfamily superfamilyc.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
家族 Family familyc.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
结构域编号 domain_idd1brwa3
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamilyd.41.3 — Pyrimidine nucleoside phosphorylase C-terminal domain
家族 Family familyd.41.3.1 — Pyrimidine nucleoside phosphorylase C-terminal domain
结构域编号 domain_idd1brwb1
类 Class classa — All alpha proteins
折叠类型 Fold folda.46 — Methionine synthase domain-like
超家族 Superfamily superfamilya.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
家族 Family familya.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
结构域编号 domain_idd1brwb2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
超家族 Superfamily superfamilyc.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
家族 Family familyc.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
结构域编号 domain_idd1brwb3
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamilyd.41.3 — Pyrimidine nucleoside phosphorylase C-terminal domain
家族 Family familyd.41.3.1 — Pyrimidine nucleoside phosphorylase C-terminal domain

CATH v4.4 (6 domains)

结构域编号 domain_id1brwA01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily30 — Pyrimidine nucleoside phosphorylase-like, C-terminal domain
结构域编号 domain_id1brwA02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
结构域编号 domain_id1brwA03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C
结构域编号 domain_id1brwB01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily30 — Pyrimidine nucleoside phosphorylase-like, C-terminal domain
结构域编号 domain_id1brwB02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
结构域编号 domain_id1brwB03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C
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8. 引用文献 (1)

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9. 文件与曲线 (10)