1rqc

;Crystals of peptide deformylase from Plasmodium falciparum with ten subunits per asymmetric unit reveal critical characteristics of the active site for drug design ;

Method: X-RAY DIFFRACTION D_max: 165.3 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	1rqc
沉积日期 deposition_date	2003-12-04
结构标题 title	;Crystals of peptide deformylase from Plasmodium falciparum with ten subunits per asymmetric unit reveal critical characteristics of the active site for drug design ;
关键词 keywords	HYDROLASE; HYDROLASE
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	51.00 Å
回转半径 Rg (电子) rg_electron	50.71 Å
零角强度 I(0) i0	577790000.00
分子量 molecular_weight	205340.0 kDa
排除体积 excluded_volume	259500 Å³
包络体积 envelope_volume	404900 Å³
水化壳体积 shell_volume	67561 Å³
包络直径 envelope_diameter	171.1 Å
壳层 Rg shell_rg	54.87 Å
包络 Rg envelope_rg	47.63 Å
形状 Rg shape_rg	50.74 Å
总 Rg total_rg	50.76 Å
总原子数 total_atoms	14349
残基数 n_residues	1700
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	165.3 Å
Rg (实空间) rg_real	50.85 Å
Rg 误差 (实空间) rg_real_error	1.48 Å
I(0) (实空间) i0_real	5.7780e+08
I(0) 误差 (实空间) i0_real_error	1.0690e+07
Rg (倒空间) rg_reciprocal	51.10 Å
I(0) (倒空间) i0_reciprocal	578000000.0000
解质量估计 total_estimate	0.8954
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	69.3 Å
偏度 Skewness skewness	0.043
峰度 Kurtosis kurtosis	-0.611
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	17890000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.883

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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 (3)

Entity 1 polymer

描述 description	formylmethionine deformylase
分子量 formula_weight	22048.0 kDa
来源方法 src_method	man
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J
原子数 atom_count	14498

DEIKIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYKATHSEEPLEHHHHHH

来源 Source

来源生物 organism	Plasmodium falciparum
通用名 common_name	malaria parasite P. falciparum
NCBI 分类编号 ncbi_taxonomy_id	5833
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	COBALT (II) ION
分子量 formula_weight	58.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 3 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	149

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6. 折叠分类 (SCOP + CATH) 23 domains

SCOP 2.08 (13 domains)

结构域编号 domain_id	d1rqca1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.167 — Peptide deformylase
超家族 Superfamily superfamily	d.167.1 — Peptide deformylase
家族 Family family	d.167.1.1 — Peptide deformylase

结构域编号 domain_id	d1rqca2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1rqcb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.167 — Peptide deformylase
超家族 Superfamily superfamily	d.167.1 — Peptide deformylase
家族 Family family	d.167.1.1 — Peptide deformylase

结构域编号 domain_id	d1rqcb2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1rqcc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.167 — Peptide deformylase
超家族 Superfamily superfamily	d.167.1 — Peptide deformylase
家族 Family family	d.167.1.1 — Peptide deformylase

结构域编号 domain_id	d1rqcd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.167 — Peptide deformylase
超家族 Superfamily superfamily	d.167.1 — Peptide deformylase
家族 Family family	d.167.1.1 — Peptide deformylase

结构域编号 domain_id	d1rqce1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.167 — Peptide deformylase
超家族 Superfamily superfamily	d.167.1 — Peptide deformylase
家族 Family family	d.167.1.1 — Peptide deformylase

结构域编号 domain_id	d1rqce2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1rqcf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.167 — Peptide deformylase
超家族 Superfamily superfamily	d.167.1 — Peptide deformylase
家族 Family family	d.167.1.1 — Peptide deformylase

结构域编号 domain_id	d1rqcg_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.167 — Peptide deformylase
超家族 Superfamily superfamily	d.167.1 — Peptide deformylase
家族 Family family	d.167.1.1 — Peptide deformylase

结构域编号 domain_id	d1rqch_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.167 — Peptide deformylase
超家族 Superfamily superfamily	d.167.1 — Peptide deformylase
家族 Family family	d.167.1.1 — Peptide deformylase

结构域编号 domain_id	d1rqci_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.167 — Peptide deformylase
超家族 Superfamily superfamily	d.167.1 — Peptide deformylase
家族 Family family	d.167.1.1 — Peptide deformylase

结构域编号 domain_id	d1rqcj_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.167 — Peptide deformylase
超家族 Superfamily superfamily	d.167.1 — Peptide deformylase
家族 Family family	d.167.1.1 — Peptide deformylase

CATH v4.4 (10 domains)

结构域编号 domain_id	1rqcA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	45 — Peptide Deformylase
同源超家族 H-superfamily homologous superfamily	10 — Peptide deformylase

结构域编号 domain_id	1rqcB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	45 — Peptide Deformylase
同源超家族 H-superfamily homologous superfamily	10 — Peptide deformylase

结构域编号 domain_id	1rqcC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	45 — Peptide Deformylase
同源超家族 H-superfamily homologous superfamily	10 — Peptide deformylase

结构域编号 domain_id	1rqcD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	45 — Peptide Deformylase
同源超家族 H-superfamily homologous superfamily	10 — Peptide deformylase

结构域编号 domain_id	1rqcE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	45 — Peptide Deformylase
同源超家族 H-superfamily homologous superfamily	10 — Peptide deformylase

结构域编号 domain_id	1rqcF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	45 — Peptide Deformylase
同源超家族 H-superfamily homologous superfamily	10 — Peptide deformylase

结构域编号 domain_id	1rqcG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	45 — Peptide Deformylase
同源超家族 H-superfamily homologous superfamily	10 — Peptide deformylase

结构域编号 domain_id	1rqcH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	45 — Peptide Deformylase
同源超家族 H-superfamily homologous superfamily	10 — Peptide deformylase

结构域编号 domain_id	1rqcI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	45 — Peptide Deformylase
同源超家族 H-superfamily homologous superfamily	10 — Peptide deformylase

结构域编号 domain_id	1rqcJ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	45 — Peptide Deformylase
同源超家族 H-superfamily homologous superfamily	10 — Peptide deformylase

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7. 引用文献 (2)

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晶胞边长 a length_a	121.263 Å
晶胞边长 b length_b	121.263 Å
晶胞边长 c length_c	177.272 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	40

空间群 space_group	P 41
空间群编号 int_tables_number	76
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2276
R_work r_work	0.2249
R_free r_free	0.2770

fit	/app/data/saxs_computation/rq/1rqc/1rqc.fit
pddf	/app/data/pr_computation/rq/1rqc/1rqc.pr.out
profile	/app/data/saxs_computation/rq/1rqc/1rqc.dat