SAXSdb — 1jcq

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jcq
沉积日期 deposition_date	2001-06-11
结构标题 title	;CRYSTAL STRUCTURE OF HUMAN PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH FARNESYL DIPHOSPHATE AND THE PEPTIDOMIMETIC INHIBITOR L-739,750 ;
关键词 keywords	;FTASE, PFT, PFTASE, FT, FPT, FARNESYLTRANSFERASE, FARNESYL TRANSFERASE, FARNESYL PROTEIN TRANSFERASE, CAAX, RAS, CANCER, TUMOR REGRESSION, L-739, 750, PEPTIDOMIMETIC, INHIBITOR, 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	27.20 Å
回转半径 Rg (电子) rg_electron	26.22 Å
零角强度 I(0) i0	114434000.00
分子量 molecular_weight	84895.0 kDa
排除体积 excluded_volume	106260 Å³
包络体积 envelope_volume	123330 Å³
水化壳体积 shell_volume	37523 Å³
包络直径 envelope_diameter	93.7 Å
壳层 Rg shell_rg	35.00 Å
包络 Rg envelope_rg	26.63 Å
形状 Rg shape_rg	26.22 Å
总 Rg total_rg	27.03 Å
总原子数 total_atoms	5984
残基数 n_residues	723
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	89.0 Å
Rg (实空间) rg_real	27.08 Å
Rg 误差 (实空间) rg_real_error	0.49 Å
I(0) (实空间) i0_real	1.1440e+08
I(0) 误差 (实空间) i0_real_error	1.5630e+06
Rg (倒空间) rg_reciprocal	27.12 Å
I(0) (倒空间) i0_reciprocal	114400000.0000
解质量估计 total_estimate	0.8872
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	33.8 Å
偏度 Skewness skewness	0.258
峰度 Kurtosis kurtosis	-0.325
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	46310000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.993

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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 (8)

Entity 1 polymer

描述 description	PROTEIN FARNESYLTRANSFERASE, ALPHA SUBUNIT
分子量 formula_weight	44864.8 kDa
EC 编号 ec_number	2.5.1.-
突变 mutation	GLU-GLU-PHE TAG ON THE C-TERMINUS
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	6318

MAATEGVGEAAQGGEPGQPAQPPPQPHPPPPQQQHKEEMAAEAGEAVASPMDDGFVSLDSPSYVLYRDRAEWADIDPVPQNDGPNPVVQIIYSDKFRDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCEILAKEKDTIRKEYWRYIGRSLQSKHSTENDSPTNVQQEEF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	PROTEIN FARNESYLTRANSFERASE, BETA SUBUNIT
分子量 formula_weight	48822.4 kDa
EC 编号 ec_number	2.5.1.-
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	B

MASPSSFTYYCPPSSSPVWSEPLYSLRPEHARERLQDDSVETVTSIEQAKVEEKIQEVFSSYKFNHLVPRLVLQREKHFHYLKRGLRQLTDAYECLDASRPWLCYWILHSLELLDEPIPQIVATDVCQFLELCQSPEGGFGGGPGQYPHLAPTYAAVNALCIIGTEEAYDIINREKLLQYLYSLKQPDGSFLMHVGGEVDVRSAYCAASVASLTNIITPDLFEGTAEWIARCQNWEGGIGGVPGMEAHGGYTFCGLAALVILKRERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQHFGSGAMLHDVVLGVPENALQPTHPVYNIGPDKVIQATTYFLQKPVPGFEELKDETSAEPATD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 branched

描述 description	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	ACETIC ACID
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	FARNESYL DIPHOSPHATE
分子量 formula_weight	382.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	2(S)-{2(S)-[2(R)-AMINO-3-MERCAPTO]PROPYLAMINO-3(S)-METHYL}PENTYLOXY-3-PHENYLPROPIONYLMETHIONINE SULFONE
分子量 formula_weight	517.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 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	334

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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	d1jcqa_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.118 — alpha-alpha superhelix
超家族 Superfamily superfamily	a.118.6 — Protein prenylyltransferase
家族 Family family	a.118.6.1 — Protein prenylyltransferase

结构域编号 domain_id	d1jcqb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.102 — alpha/alpha toroid
超家族 Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
家族 Family family	a.102.4.3 — Protein prenyltransferases

CATH v4.4 (2 domains)

结构域编号 domain_id	1jcqA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	120 — Protein prenylyltransferase

结构域编号 domain_id	1jcqB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	50 — Alpha/alpha barrel
拓扑 Topology topology	10 — Glycosyltransferase
同源超家族 H-superfamily homologous superfamily	20 —

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7. 引用文献 (3)

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晶胞边长 a length_a	178.476 Å
晶胞边长 b length_b	178.476 Å
晶胞边长 c length_c	64.842 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	6

空间群 space_group	P 61
空间群编号 int_tables_number	169
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.1790
R_work r_work	0.1790
R_free r_free	0.2090

fit	/app/data/saxs_computation/jc/1jcq/1jcq.fit
pddf	/app/data/pr_computation/jc/1jcq/1jcq.pr.out
profile	/app/data/saxs_computation/jc/1jcq/1jcq.dat

;CRYSTAL STRUCTURE OF HUMAN PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH FARNESYL DIPHOSPHATE AND THE PEPTIDOMIMETIC INHIBITOR L-739,750 ;

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 (8)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 branched

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 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 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)