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4daa

CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE IN PYRIDOXAL-5'-PHOSPHATE (PLP) FORM

Method: X-RAY DIFFRACTION Dmax: 82.2 Å Quality: GOOD
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1. 蛋白身份与相关结构 Protein Identity & Related Structures

D-AMINO ACID AMINOTRANSFERASE

Bacillus sp.

UniProt P19938

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 1–277 链 B； UniProt 1–277 未记录 SO4 SULFATE ION × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 8；PROTEIN WAS CONCENTRATED TO 30 MG/ML IN 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.6 CONTAINING 50 UM PLP AND 0.001 BETA-MERCAPTOETHANOL. CRYSTALS WERE THEN GROWN BY THE HANGING DROP METHOD IN 25% PEG 4000, 200 MM AMMONIUM SULFATE, 100 MM SODIUM ACETATE, 1 MM ALPHA-KETOGLUTARATE, AND 0.1 M TRIS-CHLORIDE PH 8.5., vapor diffusion - hanging drop 分辨率 2.40 Å R-free 0.247

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 4DAA 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
1A0G L201A MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAMINE-5'-PHOSPHATE 提交 1997-11-30 构建体不同 突变/修饰不同 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 1–282（282 aa）
链 B 1–282（282 aa）
突变：L201A 突变：L201A PMP 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray结晶条件 pH 9；THE PROTEIN WAS PRE-INCUBATED WITH 50MM D-ALANINE AND 50MM ALPHA-KETOGLUTARATE TO CONVERT PLP INTO PMP. THE PROTEIN WAS CRYSTALLIZED FROM 30% PEG3350, 500MM SODIUM ACETATE, 100MM TRIS/HCL, 5MM SODIUM AZIDE, PH9.0
分辨率 2.00 Å R-free 0.263
1DAA CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE 提交 1995-06-09 构建体不同 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 1–282（282 aa）
链 B 1–282（282 aa）
未记录 PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION mmCIF 未提供已读取条件 分辨率 1.94 Å
2DAA CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY D-CYCLOSERINE 提交 1997-10-27 构建体不同 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 1–282（282 aa）
链 B 1–282（282 aa）
未记录 DCS D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE × 2 X-RAY DIFFRACTION
X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；PROTEIN CONCENTRATED TO 30 MG/ ML IN 0.1 M POTASSIUM PHOSPHATE BUFFER PH 7.6 CONTAINING 50 UM PLP AND 0.001 BETA-MERCAPTOETHANOL. CRYSTALS WERE THEN GROWN BY THE HANGING DROP METHOD IN 22-26% PEG 4000, 0.2-0.3 M SODIUM ACETATE, 25 MM CYCLOSERINE AND 0.1 M TRIS-CHLORIDE PH 8.5., vapor diffusion - hanging drop
分辨率 2.10 Å R-free 0.260
2DAB L201A MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE 提交 1997-11-30 构建体不同 突变/修饰不同 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 1–282（282 aa）
链 B 1–282（282 aa）
突变：L201A 突变：L201A PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray结晶条件 pH 9；THE PROTEIN WAS CRYSTALLIZED FROM 30% PEG3350, 500MM SODIUM ACETATE, 100MM TRIS/HCL, 5MM SODIUM AZIDE, PH9.0
分辨率 2.00 Å R-free 0.273
3DAA CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE 提交 1998-01-20 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 1–277（277 aa）
链 B 1–277（277 aa）
未记录 PDD N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE × 2 X-RAY DIFFRACTION
X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；PDA INACTIVATED PROTEIN WAS CONCENTRATED TO 30 MG/ML IN 0.1 M POTASSIUM PHOSPHATE BUFFER PH 7.6 CONTAINING 50 UM PLP AND 0.001 BETA-MERCAPTOETHANOL. CRYSTALS WERE THEN GROWN BY THE HANGING DROP METHOD IN 27% PEG 4000, 0.3 M SODIUM ACETATE, AND 0.1 M TRIS-CHLORIDE PH 8.5., vapor diffusion - hanging drop
分辨率 1.90 Å R-free 0.245
3LQS Complex Structure of D-Amino Acid Aminotransferase and 4-amino-4,5-dihydro-thiophenecarboxylic acid (ADTA) 提交 2010-02-10 构建体不同 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 2–281（280 aa）
链 B 2–281（280 aa）
未记录 PSZ 4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]THIOPHENE-2-CARBOXYLIC ACID × 2 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Crystals were grown by the hanging drop method . The enzyme was dialyzed in 0.2 M potassium phosphate buffer pH 7.2, concentrated to 40mg/mL, and incubated with an R-ADTA:protein molecular ratio of 200:1 prior to crystallization. The enzyme solution was mixed with crystallization buffer at pH 8.5 and incubated initially at 30-40 C, then allowed to return to room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
分辨率 1.90 Å R-free 0.196
5DAA E177K MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAMINE-5'-PHOSPHATE 提交 1998-12-13 构建体不同 突变/修饰不同 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 2–278（277 aa）
链 B 2–278（277 aa）
突变：E177K 突变：E177K PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.5；PDA INACTIVATED PROTEIN WAS CONCENTRATED TO 30 MG/ML IN 0.1 M POTASSIUM PHOSPHATE BUFFER PH 7.6 CONTAINING 50 UM PLP AND 0.001 BETA-MERCAPTOETHANOL. CRYSTALS WERE THEN GROWN BY THE HANGING DROP METHOD IN 27% PEG 4000, 0.4 M SODIUM ACETATE, AND 0.1 M TRIS-CHLORIDE PH 8.5., vapor diffusion - hanging drop
分辨率 2.90 Å R-free 0.245

共 7 个其他 PDB 条目、7 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 DAAA_BACYM
Isoform —
PDB实体 1
链与序列区间 作者链 A； PDB构建体 1–277； UniProt 1–277 作者链 B； PDB构建体 1–277； UniProt 1–277

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 4daa

P(r) 距离分布 P(r) Distribution

P(r) distribution for 4daa
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id4daa
沉积日期 deposition_date1998-01-26
结构标题 titleCRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE IN PYRIDOXAL-5'-PHOSPHATE (PLP) FORM
关键词 keywordsAMINOTRANSFERASE, PYRIDOXAL PHOSPHATE, TRANSAMINASE; AMINOTRANSFERASE
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_guinier26.11 Å
回转半径 Rg (电子) rg_electron25.41 Å
零角强度 I(0) i066563200.00
分子量 molecular_weight63997.0 kDa
排除体积 excluded_volume80316 ų
包络体积 envelope_volume94175 ų
水化壳体积 shell_volume30850 ų
包络直径 envelope_diameter84.5 Å
壳层 Rg shell_rg32.93 Å
包络 Rg envelope_rg25.60 Å
形状 Rg shape_rg25.39 Å
总 Rg total_rg26.29 Å
总原子数 total_atoms4506
残基数 n_residues554
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 dmax82.2 Å
Rg (实空间) rg_real26.09 Å
Rg 误差 (实空间) rg_real_error0.50 Å
I(0) (实空间) i0_real6.6560e+07
I(0) 误差 (实空间) i0_real_error8.4630e+05
Rg (倒空间) rg_reciprocal26.10 Å
I(0) (倒空间) i0_reciprocal66560000.0000
解质量估计 total_estimate0.8983
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary28.3 Å
偏度 Skewness skewness0.348
峰度 Kurtosis kurtosis-0.391
角度范围 angular_range— – 0.3050 Å−1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha32570000.0000
实空间数据点数 n_real_points62
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.924
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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) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_idd4daaa_
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
超家族 Superfamily superfamilye.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
家族 Family familye.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
结构域编号 domain_idd4daab_
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
超家族 Superfamily superfamilye.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
家族 Family familye.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

CATH v4.4 (4 domains)

结构域编号 domain_id4daaA01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain
结构域编号 domain_id4daaA02
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology10 — D-amino Acid Aminotransferase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — D-amino Acid Aminotransferase, subunit A, domain 2
结构域编号 domain_id4daaB01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain
结构域编号 domain_id4daaB02
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology10 — D-amino Acid Aminotransferase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — D-amino Acid Aminotransferase, subunit A, domain 2
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8. 引用文献 (2)

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9. 文件与曲线 (10)