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1c7s

BETA-N-ACETYLHEXOSAMINIDASE MUTANT D539A COMPLEXED WITH DI-N-ACETYL-BETA-D-GLUCOSAMINE (CHITOBIASE)

Method: X-RAY DIFFRACTION Dmax: 88.6 Å Quality: GOOD
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1. 蛋白身份与相关结构 Protein Identity & Related Structures

BETA-N-ACETYLHEXOSAMINIDASE

Serratia marcescens

UniProt Q54468

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 其他组合 同源多聚体 蛋白 × 2 其他聚合物 2 PDB 声明：dimeric（2） 与蛋白拷贝数一致 链 A； UniProt 28–885 片段：MATURE PROTEIN, PERIPLASMATIC TARGETING SEQUENCE RESIDUES 1-27 CLEAVED OFF DURING MATURATION 突变：D539A 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 8 X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 4.8；CO-CRYSTALS WERE GROWN BY THE HANGING-DROP VAPOR DIFFUSION METHOD. RESERVOIR BUFFER CONTAINED 2.3 MOLAR AMMONIUM SULFATE AND 100 MILLIMOLAR CACODYLATE BUFFER PH 4.8. PROTEIN SOLUTION 40 MILLIGRAM PER MILLILITER WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR CONTAINING 10 MILLIMOLAR DI-NAG. CRYSTALS ABOUT 0.5 X 0.2 X 0.2 MILLIMETER IN SIZE WERE FORMED WITHIN 2-3 DAYS., VAPOR DIFFUSION, HANGING DROP 分辨率 1.80 Å R-free 0.224

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 1C7S 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
1C7T BETA-N-ACETYLHEXOSAMINIDASE MUTANT E540D COMPLEXED WITH DI-N ACETYL-D-GLUCOSAMINE (CHITOBIASE) 提交 2000-03-17 突变/修饰不同 结构质量不同 Assembly 1 其他组合 同源多聚体；蛋白 × 2 PDB 声明：dimeric
链 A 28–885（858 aa） 片段：MATURE PROTEIN, PERIPLASMATIC TARGETING SEQUENCE RESIDUES 1-27 CLEAVED OFF DURING MATURATION
突变：YES SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.8；CO-CRYSTALS WERE GROWN BY THE HANGING-DROP VAPOR DIFFUSION METHOD. RESERVOIR BUFFER CONTAINED 2.3 MOLAR AMMONIUM SULFATE AND 100 MILLIMOLAR CACODYLATE BUFFER PH 4.8. PROTEIN SOLUTION 40 MILLIGRAM PER MILLILITER WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR CONTAINING 10 MILLIMOLAR DI-NAG. CRYSTALS ABOUT 0.5 X 0.2 X 0.2 MILLIMETER IN SIZE WERE FORMED WITHIN 2-3 DAYS., VAPOR DIFFUSION, HANGING DROP
分辨率 1.90 Å R-free 0.246
1QBA BACTERIAL CHITOBIASE, GLYCOSYL HYDROLASE FAMILY 20 提交 1996-06-06 构建体不同 突变/修饰不同 聚集状态不同 配体/离子不同 实验环境不同 结构质量不同 Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric
链 A 28–885（858 aa）
未记录 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.6；CRYSTAL WERE GROWN AT ROOM TEMPERATURE FROM HANGING DROPS CONTAINING 62% SATURATED AMMONIUM SULFATE, 1.5% ISOPROPANOL AND 100 MM CACODYLATE, PH 5.6., vapor diffusion - hanging drop
分辨率 1.85 Å R-free 0.196
1QBB BACTERIAL CHITOBIASE COMPLEXED WITH CHITOBIOSE (DINAG) 提交 1996-06-07 构建体不同 突变/修饰不同 聚集状态不同 配体/离子不同 实验环境不同 结构质量不同 Assembly 1 其他组合 单体；蛋白 × 1 PDB 声明：monomeric
链 A 28–885（858 aa）
未记录 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.6；CRYSTAL WERE GROWN AT ROOM TEMPERATURE FROM HANGING DROPS CONTAINING 62% SATURATED AMMONIUM SULFATE, 1.5% ISOPROPANOL AND 100 MM CACODYLATE, PH 5.6. DERIVATIZATION CONDITIONS: SOLID CHITOBIOSE WAS ADDED TO THE MOTHER LIQUOR TO MAKE UP HIGH CONCENTRATED STOCK SOLUTION, 0.5 TO 1.0 MICRO LITERS OF THE STOCK SOLUTION WERE ADDED TO THE CRYSTALLISATION DROP CONTAINING CRYSTALS. THE CRYSTALS WERE MOUNTED IMMEDIATELY IN GLASS CAPILLARY. EXPOSURE TIME WAS LIMITED TO 10 MINUTES OR LESS. THESE CRYSTALS: 4 MINS 50 SECS. THE CHITOBIOSE WAS SUPPLIED BY SIGMA., vapor diffusion - hanging drop
分辨率 2.00 Å R-free 0.212

共 3 个其他 PDB 条目、3 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 CHB_SERMA
Isoform —
PDB实体 1
链与序列区间 作者链 A； PDB构建体 1–858； UniProt 28–885

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 1c7s

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1c7s
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id1c7s
沉积日期 deposition_date2000-03-14
结构标题 titleBETA-N-ACETYLHEXOSAMINIDASE MUTANT D539A COMPLEXED WITH DI-N-ACETYL-BETA-D-GLUCOSAMINE (CHITOBIASE)
关键词 keywords;GLYCOSYL HYDROLASE, BETA-N-ACETYLHEXOSAMINIDASE, CHITINOLYSIS, A/B(TIM)-BARREL, SITE DIRECTED MUTAGENESIS, SUBSTRATE NUCLEOPHILE STABILIZER MUTATION, HYDROLASE ;; HYDROLASE
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_guinier28.57 Å
回转半径 Rg (电子) rg_electron27.62 Å
零角强度 I(0) i0152427000.00
分子量 molecular_weight96623.0 kDa
排除体积 excluded_volume120210 ų
包络体积 envelope_volume139350 ų
水化壳体积 shell_volume40429 ų
包络直径 envelope_diameter94.8 Å
壳层 Rg shell_rg36.33 Å
包络 Rg envelope_rg28.01 Å
形状 Rg shape_rg27.57 Å
总 Rg total_rg28.56 Å
总原子数 total_atoms6816
残基数 n_residues858
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 dmax88.6 Å
Rg (实空间) rg_real28.45 Å
Rg 误差 (实空间) rg_real_error0.46 Å
I(0) (实空间) i0_real1.5240e+08
I(0) 误差 (实空间) i0_real_error2.0000e+06
Rg (倒空间) rg_reciprocal28.50 Å
I(0) (倒空间) i0_reciprocal152400000.0000
解质量估计 total_estimate0.8999
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary34.8 Å
偏度 Skewness skewness0.219
峰度 Kurtosis kurtosis-0.397
角度范围 angular_range— – 0.2800 Å−1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha30410000.0000
实空间数据点数 n_real_points57
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.941
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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 (4)

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7. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_idd1c7sa1
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.18 — E set domains
家族 Family familyb.1.18.2 — E-set domains of sugar-utilizing enzymes
结构域编号 domain_idd1c7sa2
类 Class classb — All beta proteins
折叠类型 Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
超家族 Superfamily superfamilyb.2.2 — Carbohydrate-binding domain
家族 Family familyb.2.2.3 — Bacterial chitobiase, n-terminal domain
结构域编号 domain_idd1c7sa3
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamilyc.1.8 — (Trans)glycosidases
家族 Family familyc.1.8.6 — beta-N-acetylhexosaminidase catalytic domain
结构域编号 domain_idd1c7sa4
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.92 — Zincin-like
超家族 Superfamily superfamilyd.92.2 — beta-N-acetylhexosaminidase-like domain
家族 Family familyd.92.2.1 — beta-N-acetylhexosaminidase domain

CATH v4.4 (4 domains)

结构域编号 domain_id1c7sA01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily290 —
结构域编号 domain_id1c7sA02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology379 — Chitobiase; domain 2
同源超家族 H-superfamily homologous superfamily10 — Chitobiase/beta-hexosaminidase domain 2-like
结构域编号 domain_id1c7sA03
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily80 — Glycosidases
结构域编号 domain_id1c7sA04
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
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8. 引用文献 (2)

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9. 文件与曲线 (10)