SAXSdb — 1pdh

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1pdh
沉积日期 deposition_date	1994-12-01
结构标题 title	;CRYSTAL STRUCTURE OF P-HYDROXYBENZOATE HYDROXYLASE RECONSTITUTED WITH THE MODIFIED FAD PRESENT IN ALCOHOL OXIDASE FROM METHYLOTROPHIC YEASTS: EVIDENCE FOR AN ARABINOFLAVIN ;
关键词 keywords	OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

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

回转半径 Rg (Guinier) rg_guinier	22.52 Å
回转半径 Rg (电子) rg_electron	21.49 Å
零角强度 I(0) i0	34607000.00
分子量 molecular_weight	44856.0 kDa
排除体积 excluded_volume	55969 Å³
包络体积 envelope_volume	64684 Å³
水化壳体积 shell_volume	24861 Å³
包络直径 envelope_diameter	72.8 Å
壳层 Rg shell_rg	28.54 Å
包络 Rg envelope_rg	21.69 Å
形状 Rg shape_rg	21.50 Å
总 Rg total_rg	22.32 Å
总原子数 total_atoms	3161
残基数 n_residues	391
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

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

最大尺寸 Dmax dmax	70.9 Å
Rg (实空间) rg_real	22.46 Å
Rg 误差 (实空间) rg_real_error	0.35 Å
I(0) (实空间) i0_real	3.4610e+07
I(0) 误差 (实空间) i0_real_error	4.2150e+05
Rg (倒空间) rg_reciprocal	22.47 Å
I(0) (倒空间) i0_reciprocal	34610000.0000
解质量估计 total_estimate	0.8964
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	25.8 Å
偏度 Skewness skewness	0.304
峰度 Kurtosis kurtosis	-0.373
角度范围 angular_range	— – 0.3550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11260000.0000
实空间数据点数 n_real_points	67
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.959

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

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5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	P-HYDROXYBENZOATE HYDROXYLASE
分子量 formula_weight	44380.6 kDa
EC 编号 ec_number	1.14.13.2
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	3445

MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAGVDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERVYPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLTEKVEDWSDERFWTELKARLPAEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFSQRIQQTELEYYLGSEAGLATIAENYVGLPYEEIE

来源 Source

来源生物 organism	Pseudomonas fluorescens
NCBI 分类编号 ncbi_taxonomy_id	294

Entity 2 non-polymer

描述 description	ARABINO-FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	P-HYDROXYBENZOIC ACID
分子量 formula_weight	138.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	284

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1pdha1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1pdha2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.2 — PHBH-like

CATH v4.4 (2 domains)

结构域编号 domain_id	1pdhA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1pdhA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

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7. 引用文献 (12)

;Crystal structure of p-hydroxybenzoate hydroxylase reconstituted with the modified FAD present in alcohol oxidase from methylotrophic yeasts: evidence for an arabinoflavin. ;

Protein Sci. (1994)

PMID: 7756982 PRIMARY

;Crystal Structure of Wild-Type P-Hydroxybenzoate Hydroxylase Complexed with 4-Aminobenzoate, 2,4-Dihydroxybenzoate and 2-Hydroxy-4-Aminobenzoate. Evidence for a Proton Channel and a New Binding Mode of the Flavin Ring ;

Biochemistry (1994)

Crystal Structure of the Reduced Form of P-Hydroxybenzoate Hydroxylase Refine at 2.3 Angstroms Resolution

Proteins (1992)

Crystal Structure of the P-Hydroxybenzoate Hydroxylase-Substrate Complex Refined at 1.9 Angstroms Resolution

J.Mol.Biol. (1989)

Analysis of the Active Site of the Flavoprotein P-Hydroxybenzoate Hydroxylase and Some Ideas with Respect to its Reaction Mechanism

Biochemistry (1989)

;The Coenzyme Analogue Adenosine 5-Diphosphoribose Displaces the Fad from the Active Site of P-Hydroxybenzoate Hydroxylase. An X-Ray Crystallographic Investigation ;

Biochemistry (1989)

The Influence of Purification and Protein Heterogeneity on the Crystallization of P-Hydroxybenzoate Hydroxylase

Eur.J.Biochem. (1989)

Crystal Structure of P-Hydroxybenzoate Hydroxylase Complexed with its Reaction Product 3,4-Dihydroxybenzoate

J.Mol.Biol. (1988)

;Molecular Modeling Reveals the Possible Importance of a Carbonyl Oxygen Binding Pocket for the Catalytic Mechanism of P-Hydroxybenzoate Hydroxylase ;

J.Biol.Chem. (1988)

;Comparison of the Three-Dimensional Protein and Nucleotide Structure of the Fad-Binding Domain of P-Hydroxybenzoate Hydroxylase with the Fad-as Well as Nadph-Binding Domains of Glutathione Reductase ;

J.Mol.Biol. (1983)

Crystal Structure of P-Hydroxybenzoate Hydroxylase

J.Mol.Biol. (1979)

Crystallization and Preliminary X-Ray Investigation of P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens

J.Biol.Chem. (1975)

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晶胞边长 a length_a	72.100 Å
晶胞边长 b length_b	146.400 Å
晶胞边长 c length_c	88.450 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	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	0.1790
R_work r_work	0.1790
R_free r_free	—

fit	/app/data/saxs_computation/pd/1pdh/1pdh.fit
pddf	/app/data/pr_computation/pd/1pdh/1pdh.pr.out
profile	/app/data/saxs_computation/pd/1pdh/1pdh.dat

;CRYSTAL STRUCTURE OF P-HYDROXYBENZOATE HYDROXYLASE RECONSTITUTED WITH THE MODIFIED FAD PRESENT IN ALCOHOL OXIDASE FROM METHYLOTROPHIC YEASTS: EVIDENCE FOR AN ARABINOFLAVIN ;

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution