1ltx

Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid

Method: X-RAY DIFFRACTION D_max: 144.8 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	1ltx
沉积日期 deposition_date	2002-05-21
结构标题 title	Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid
关键词 keywords	RAB PRENYLATION, PRENYLTRANSFERASE, LUCINE-RICH REPEATS, POST-TRANSLATIONAL MODIFICATION, Transferase-Protein binding COMPLEX; Transferase/Protein binding
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	41.19 Å
回转半径 Rg (电子) rg_electron	40.88 Å
零角强度 I(0) i0	353185000.00
分子量 molecular_weight	153210.0 kDa
排除体积 excluded_volume	191630 Å³
包络体积 envelope_volume	248750 Å³
水化壳体积 shell_volume	52603 Å³
包络直径 envelope_diameter	152.4 Å
壳层 Rg shell_rg	44.25 Å
包络 Rg envelope_rg	40.49 Å
形状 Rg shape_rg	40.86 Å
总 Rg total_rg	41.15 Å
总原子数 total_atoms	10750
残基数 n_residues	1352
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	144.8 Å
Rg (实空间) rg_real	41.37 Å
Rg 误差 (实空间) rg_real_error	1.56 Å
I(0) (实空间) i0_real	3.5320e+08
I(0) 误差 (实空间) i0_real_error	6.7960e+06
Rg (倒空间) rg_reciprocal	41.19 Å
I(0) (倒空间) i0_reciprocal	353100000.0000
解质量估计 total_estimate	0.8579
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	41.9 Å
偏度 Skewness skewness	0.464
峰度 Kurtosis kurtosis	-0.268
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	43500000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.808

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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	RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT
分子量 formula_weight	64981.2 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	A
原子数 atom_count	10874

MHGRLKVKTSEEQAEAKRLEREQKLKLYQSATQAVFQKRQAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPHDVLCCVHVSREEACLSVCFSRPLTVGSRMGTLLLMVDEAPLSVEWRTPDGRNRPSHVWLCDLPAASLNDQLPQHTFRVIWTGSDSQKECVLLKDRPECWCRDSATDEQLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDDLRSKFLLENSVLKMEYADVRVLHLAHKDLTVLCHLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVDGVANLPRLQELLLCNNRLQQSAAIQPLVSCPRLVLLNLQGNSLCQEEGIQERLAEMLPSVSSILT

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT
分子量 formula_weight	36892.2 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

MGTQQKDVTIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGVYWGLTVMDLMGQLHRMNKEEILVFIKSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQIKPVSPVFCMPEEVLQRVNVQPELVS

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	Rab Escort Protein 1
分子量 formula_weight	72594.2 kDa
突变 mutation	A473T, G483A, Q231K
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	R

MADNLPSDFDVIVIGTGLPESIIAAACSRSGQRVLHVDSRSYYGGNWASFSFSGLLSWLKEYQENNDVVTENSMWQEQILENEEAIPLSSKDKTIQHVEVFCYASQDLHKDVEEAGALQKNHASVTSAQSAEAAEAAETSCLPTAVEPLSMGSCEIPAEQSQCPGPESSPEVNDAEATGKKENSDAKSSTEEPSENVPKVQDNTETPKKNRITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGTVEQVPCSRADVFNSKQLTMVEKRMLMKFLTFCVEYEEHPDEYRAYEGTTFSEYLKTQKLTPNLQYFVLHSIAMTSETTSCTVDGLKATKKFLQCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLVVDKESRKCKAVIDQFGQRIISKHFIIEDSYLSENTCSRVQYRQISRAVLITDGSVLKTDADQQVSILTVPAEEPGSFAVRVIELCSSTMTCMKGTYLVHLTCMSSKTAREDLERVVQKLFTPYTEIEAENEQVEKPRLLWALYFNMRDSSDISRDCYNDLPSNVYVCSGPDSGLGNDNAVKQAETLFQQICPNEDFCPAPPNPEDIVLDGDSSQQEVPESSVTPETNSETPKESTVLGNPEEPSE

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Spodoptera frugiperda

Entity 4 polymer

描述 description	AAAA
分子量 formula_weight	302.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	P

AAAA

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	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	FARNESYL
分子量 formula_weight	206.4 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	103

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6. 折叠分类 (SCOP + CATH) 13 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1ltxa1
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	d1ltxa2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.7 — C2 domain-like
超家族 Superfamily superfamily	b.7.4 — Rab geranylgeranyltransferase alpha-subunit, insert domain
家族 Family family	b.7.4.1 — Rab geranylgeranyltransferase alpha-subunit, insert domain

结构域编号 domain_id	d1ltxa3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
超家族 Superfamily superfamily	c.10.2 — L domain-like
家族 Family family	c.10.2.2 — Rab geranylgeranyltransferase alpha-subunit, C-terminal domain

结构域编号 domain_id	d1ltxb_
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

结构域编号 domain_id	d1ltxr1
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.3.1.3 — GDI-like N domain

结构域编号 domain_id	d1ltxr2
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.16.1.6 — GDI-like

CATH v4.4 (7 domains)

结构域编号 domain_id	1ltxA01
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	1ltxA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1130 — Rab geranylgeranyltransferase alpha-subunit, insert domain

结构域编号 domain_id	1ltxA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	80 — Alpha-Beta Horseshoe
拓扑 Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease Inhibitor

结构域编号 domain_id	1ltxB00
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 —

结构域编号 domain_id	1ltxR01
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	1ltxR02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	519 — Guanine Nucleotide Dissociation Inhibitor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 2

结构域编号 domain_id	1ltxR03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

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7. 引用文献 (2)

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晶胞边长 a length_a	68.700 Å
晶胞边长 b length_b	197.300 Å
晶胞边长 c length_c	85.300 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	112.80 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	19.740 Å
R 因子 r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2720

fit	/app/data/saxs_computation/lt/1ltx/1ltx.fit
pddf	/app/data/pr_computation/lt/1ltx/1ltx.pr.out
profile	/app/data/saxs_computation/lt/1ltx/1ltx.dat

Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid

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 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. 折叠分类 (SCOP + CATH) 13 domains

SCOP 2.08 (6 domains)

CATH v4.4 (7 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)