1zcw

Co-crystal structure of Orf2 an aromatic prenyl transferase from Streptomyces sp. strain CL190 complexed with GPP

Method: X-RAY DIFFRACTION D_max: 60.4 Å Quality: REASONABLE

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	1zcw
沉积日期 deposition_date	2005-04-13
结构标题 title	Co-crystal structure of Orf2 an aromatic prenyl transferase from Streptomyces sp. strain CL190 complexed with GPP
关键词 keywords	novel aromatic prenyltransferase barrel fold, PT-barrel, TRANSFERASE; TRANSFERASE
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	19.49 Å
回转半径 Rg (电子) rg_electron	18.20 Å
零角强度 I(0) i0	19019100.00
分子量 molecular_weight	33601.0 kDa
排除体积 excluded_volume	42173 Å³
包络体积 envelope_volume	47270 Å³
水化壳体积 shell_volume	21054 Å³
包络直径 envelope_diameter	60.2 Å
壳层 Rg shell_rg	25.12 Å
包络 Rg envelope_rg	18.36 Å
形状 Rg shape_rg	18.21 Å
总 Rg total_rg	19.12 Å
总原子数 total_atoms	2365
残基数 n_residues	302
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	60.4 Å
Rg (实空间) rg_real	19.32 Å
Rg 误差 (实空间) rg_real_error	0.30 Å
I(0) (实空间) i0_real	1.9020e+07
I(0) 误差 (实空间) i0_real_error	2.2010e+05
Rg (倒空间) rg_reciprocal	19.34 Å
I(0) (倒空间) i0_reciprocal	19020000.0000
解质量估计 total_estimate	0.6692
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	24.7 Å
偏度 Skewness skewness	0.075
峰度 Kurtosis kurtosis	-0.481
角度范围 angular_range	— – 0.4100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6447000.0000
实空间数据点数 n_real_points	72
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 0.356; Positv: 1.000; Valcen: 0.984; Smooth: 0.000

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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 (5)

Entity 1 polymer

描述 description	Aromatic prenyltransferase
分子量 formula_weight	33778.2 kDa
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	2570

MSEAADVERVYAAMEEAAGLLGVACARDKIYPLLSTFQDTLVEGGSVVVFSMASGRHSTELDFSISVPTSHGDPYATVVEKGLFPATGHPVDDLLADTQKHLPVSMFAIDGEVTGGFKKTYAFFPTDNMPGVAELSAIPSMPPAVAENAELFARYGLDKVQMTSMDYKKRQVNLYFSELSAQTLEAESVLALVRELGLHVPNELGLKFCKRSFSVYPTLNWETGKIDRLCFAVISNDPTLVPSSDEGDIEKFHNYATKAPYAYVGEKRTLVYGLTLSPKEEYYKLGAYYHITDVQRGLLKAFDSLED

来源 Source

来源生物 organism	Streptomyces sp.
NCBI 分类编号 ncbi_taxonomy_id	93372
宿主生物 host_organism	Escherichia coli BL21

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	NITRATE ION
分子量 formula_weight	62.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	GERANYL DIPHOSPHATE
分子量 formula_weight	314.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	205

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6. 折叠分类 (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1zcwa_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.313 — Antiparallel beta/alpha barrel (PT-barrel)
超家族 Superfamily superfamily	d.313.1 — Prenyltransferase-like
家族 Family family	d.313.1.1 — Prenyltransferase-like

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7. 引用文献 (1)

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晶胞边长 a length_a	74.598 Å
晶胞边长 b length_b	91.901 Å
晶胞边长 c length_c	48.832 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	4

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.250 Å
最低分辨率 resolution_low	43.120 Å
R 因子 r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2510

fit	/app/data/saxs_computation/zc/1zcw/1zcw.fit
pddf	/app/data/pr_computation/zc/1zcw/1zcw.pr.out
profile	/app/data/saxs_computation/zc/1zcw/1zcw.dat