8y64

Crystal structure of open state ferulic acid decarboxylase from Saccharomyces cerevisiae, F397V/I398L/T438P/P441V mutant

Method: X-RAY DIFFRACTION D_max: 110.5 Å Quality: GOOD

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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8y64
沉积日期 deposition_date	2024-02-01
最后修订 last_revision	2025-01-01
结构标题 title	Crystal structure of open state ferulic acid decarboxylase from Saccharomyces cerevisiae, F397V/I398L/T438P/P441V mutant
关键词 keywords	ferulic acid decarboxylase, LYASE; LYASE
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	32.51 Å
回转半径 Rg (电子) rg_electron	31.90 Å
零角强度 I(0) i0	181519000.00
分子量 molecular_weight	112300.0 kDa
排除体积 excluded_volume	142260 Å³
包络体积 envelope_volume	169100 Å³
水化壳体积 shell_volume	44074 Å³
包络直径 envelope_diameter	112.7 Å
壳层 Rg shell_rg	38.90 Å
包络 Rg envelope_rg	31.87 Å
形状 Rg shape_rg	31.87 Å
总 Rg total_rg	32.54 Å
总原子数 total_atoms	7902
残基数 n_residues	1004
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	110.5 Å
Rg (实空间) rg_real	32.61 Å
Rg 误差 (实空间) rg_real_error	0.87 Å
I(0) (实空间) i0_real	1.8150e+08
I(0) 误差 (实空间) i0_real_error	3.0500e+06
Rg (倒空间) rg_reciprocal	32.57 Å
I(0) (倒空间) i0_reciprocal	181500000.0000
解质量估计 total_estimate	0.8632
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	36.1 Å
偏度 Skewness skewness	0.470
峰度 Kurtosis kurtosis	-0.201
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	43440000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.791; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.864

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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	Ferulic acid decarboxylase 1
分子量 formula_weight	56181.7 kDa
EC 编号 ec_number	4.1.1.102
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	8977

MRKLNPALEFRDFIQVLKDEDDLIEITEEIDPNLEVGAIMRKAYESHLPAPLFKNLKGASKDLFSILGCPAGLRSKEKGDHGRIAHHLGLDPKTTIKEIIDYLLECKEKEPLPPITVPVSSAPCKTHILSEEKIHLQSLPTPYLHVSDGGKYLQTYGMWILQTPDKKWTNWSIARGMVVDDKHITGLVIKPQHIRQIADSWAAIGKANEIPFALCFGVPPAAILVSSMPIPEGVSESDYVGAILGESVPVVKCETNDLMVPATSEMVFEGTLSLTDTHLEGPFGEMHGYVFKSQGHPCPLYTVKAMSYRDNAILPVSNPGLCTDETHTLIGSLVATEAKELAIESGLPILDAFMPYEAQALWLILKVDLKGLQALKTTPEEFCKKVGDIYFRTKVGVLVHEIILVADDIDIFNFKEVIWAYVTRHTPVADQMAFDDVPSFVLAPFVSQSSRSKTMKGGKCVTNCIFRQQYERSFDYITCNFEKGYPKGLVDKVNENWKRYGYK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 3 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 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	1059

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7. 引用文献 (1)

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晶胞边长 a length_a	81.778 Å
晶胞边长 b length_b	81.830 Å
晶胞边长 c length_c	166.321 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	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	orthorhombic

分辨率 resolution	1.970 Å
最低分辨率 resolution_low	30.810 Å
R 因子 r_factor	0.1522
R_work r_work	0.1506
R_free r_free	0.1841

fit	/app/data/saxs_computation/y6/8y64/8y64.fit
pddf	/app/data/pr_computation/y6/8y64/8y64.pr.out
profile	/app/data/saxs_computation/y6/8y64/8y64.dat

Crystal structure of open state ferulic acid decarboxylase from Saccharomyces cerevisiae, F397V/I398L/T438P/P441V mutant

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