2bf2

Crystal structure of native toluene-4-monooxygenase catalytic effector protein, T4moD

Method: X-RAY DIFFRACTION D_max: 55.7 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2bf2
沉积日期 deposition_date	2004-12-03
结构标题 title	Crystal structure of native toluene-4-monooxygenase catalytic effector protein, T4moD
关键词 keywords	;CATALYTIC EFFECTOR PROTEIN, MAD PHASING, AROMATIC HYDROCARBON CATABOLISM, OXIDOREDUCTASE, MONOOXYGENASE, TOLUENE OXIDATION, FAD, FLAVOPROTEIN, IRON ;; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	17.99 Å
回转半径 Rg (电子) rg_electron	16.67 Å
零角强度 I(0) i0	9648990.00
分子量 molecular_weight	22388.0 kDa
排除体积 excluded_volume	27807 Å³
包络体积 envelope_volume	32898 Å³
水化壳体积 shell_volume	16455 Å³
包络直径 envelope_diameter	55.0 Å
壳层 Rg shell_rg	22.72 Å
包络 Rg envelope_rg	16.91 Å
形状 Rg shape_rg	16.66 Å
总 Rg total_rg	17.69 Å
总原子数 total_atoms	1579
残基数 n_residues	201
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	55.7 Å
Rg (实空间) rg_real	17.86 Å
Rg 误差 (实空间) rg_real_error	0.30 Å
I(0) (实空间) i0_real	9.6490e+06
I(0) 误差 (实空间) i0_real_error	1.2050e+05
Rg (倒空间) rg_reciprocal	17.88 Å
I(0) (倒空间) i0_reciprocal	9649000.0000
解质量估计 total_estimate	0.9020
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	54.9 Å
偏度 Skewness skewness	0.121
峰度 Kurtosis kurtosis	-0.476
角度范围 angular_range	— – 0.4400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1734000.0000
实空间数据点数 n_real_points	75
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.988

▶

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

▶

5. 实体与聚合体信息 (2)

▼

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2bf2a_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.137 — Monooxygenase (hydroxylase) regulatory protein
超家族 Superfamily superfamily	d.137.1 — Monooxygenase (hydroxylase) regulatory protein
家族 Family family	d.137.1.1 — Monooxygenase (hydroxylase) regulatory protein

结构域编号 domain_id	d2bf2b_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.137 — Monooxygenase (hydroxylase) regulatory protein
超家族 Superfamily superfamily	d.137.1 — Monooxygenase (hydroxylase) regulatory protein
家族 Family family	d.137.1.1 — Monooxygenase (hydroxylase) regulatory protein

CATH v4.4 (2 domains)

结构域编号 domain_id	2bf2A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	56 — Phenol Hydroxylase P2 Protein
同源超家族 H-superfamily homologous superfamily	10 — Monooxygenase component MmoB/DmpM

结构域编号 domain_id	2bf2B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	56 — Phenol Hydroxylase P2 Protein
同源超家族 H-superfamily homologous superfamily	10 — Monooxygenase component MmoB/DmpM

▶

7. 引用文献 (6)

Crystal Structures and Functional Studies of T4Mod, the Toluene 4-Monooxygenase Catalytic Effector Protein

Biochemistry (2005)

PMID: 15882052 · DOI: 10.1021/BI047459G PRIMARY

;Crystallization and Preliminary Analysis of Native and N-Terminal Truncated Isoforms of Toluene-4-Monooxygenase Catalytic Effector Protein ;

Acta Crystallogr.,Sect.D (2003)

PMID: 12595730 · DOI: 10.1107/S0907444903000416

;Combined Participation of Hydroxylase Active Site Residues and Effector Protein Binding in a Para to Ortho Modulation of Toluene-4-Monooxygenase Regiospecificity ;

Biochemistry (2002)

PMID: 11863457 · DOI: 10.1021/BI012036P

Solution Structure of the Toluene-4-Monooxygenase Effector Protein (T4Mod)

Biochemistry (2001)

PMID: 11297417 · DOI: 10.1021/BI0013703

Application of Fed-Batch Fermentation to the Preparation of Isotopically Labeled or Selenomethionyl-Labeled Proteins

Protein Expr.Purif (1999)

PMID: 10336868 · DOI: 10.1006/PREP.1999.1067

;Recombinant Toluene-4-Monooxygenase: Catalytic and Mossbauer Studies of the Purified Diiron and Rieske Components of a Four-Protein Complex ;

Biochemistry (1996)

PMID: 8703915 · DOI: 10.1021/BI960456M

▶

晶胞边长 a length_a	86.671 Å
晶胞边长 b length_b	86.671 Å
晶胞边长 c length_c	144.325 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	120.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	P 61 2 2
空间群编号 int_tables_number	178
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	37.000 Å
R 因子 r_factor	0.2480
R_work r_work	0.2440
R_free r_free	0.2890

描述 description	TOLUENE-4-MONOOXYGENASE SYSTEM PROTEIN D
分子量 formula_weight	11497.8 kDa
EC 编号 ec_number	1.14.13.-
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	1637

Crystal structure of native toluene-4-monooxygenase catalytic effector protein, T4moD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

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. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. 引用文献 (6)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	PSEUDOMONAS MENDOCINA
NCBI 分类编号 ncbi_taxonomy_id	300
宿主生物 host_organism	ESCHERICHIA COLI

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	58

fit	/app/data/saxs_computation/bf/2bf2/2bf2.fit
pddf	/app/data/pr_computation/bf/2bf2/2bf2.pr.out
profile	/app/data/saxs_computation/bf/2bf2/2bf2.dat