1u2v

Crystal structure of Arp2/3 complex with bound ADP and calcium

Method: X-RAY DIFFRACTION D_max: 142.4 Å Quality: EXCELLENT

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	1u2v
沉积日期 deposition_date	2004-07-20
结构标题 title	Crystal structure of Arp2/3 complex with bound ADP and calcium
关键词 keywords	STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	43.81 Å
回转半径 Rg (电子) rg_electron	43.43 Å
零角强度 I(0) i0	538819000.00
分子量 molecular_weight	193300.0 kDa
排除体积 excluded_volume	242800 Å³
包络体积 envelope_volume	330560 Å³
水化壳体积 shell_volume	63039 Å³
包络直径 envelope_diameter	149.9 Å
壳层 Rg shell_rg	48.68 Å
包络 Rg envelope_rg	43.00 Å
形状 Rg shape_rg	43.43 Å
总 Rg total_rg	43.65 Å
总原子数 total_atoms	13608
残基数 n_residues	1714
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	142.4 Å
Rg (实空间) rg_real	43.76 Å
Rg 误差 (实空间) rg_real_error	1.04 Å
I(0) (实空间) i0_real	5.3880e+08
I(0) 误差 (实空间) i0_real_error	9.4870e+06
Rg (倒空间) rg_reciprocal	43.81 Å
I(0) (倒空间) i0_reciprocal	538800000.0000
解质量估计 total_estimate	0.9002
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	47.5 Å
偏度 Skewness skewness	0.198
峰度 Kurtosis kurtosis	-0.682
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	77320000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.914

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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 (10)

Entity 1 polymer

描述 description	Actin-Related Protein 3
分子量 formula_weight	47428.0 kDa
来源方法 src_method	nat
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	13922

MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS

Entity 2 polymer

描述 description	Actin-Related Protein 2
分子量 formula_weight	44818.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

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

MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDEASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNREKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTRRLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVLVESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKHIVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAVLADIMKDKDNFWMTRQEYQEKGVRVLEKLGVTVR

Entity 3 polymer

描述 description	Arp2/3 Complex 41Kda Subunit
分子量 formula_weight	41016.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

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

MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGNKWVQVHELKEHNGQVTGVDWAPDSNRIVTCGTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNEKKFAVGSGSRVISICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNSVLLAAGSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATLASETLPLLAVTFITESSLVAAGHDCFPVLFTYDSAAGKLSFGGRLDVPKQSSQRGLTARERFQNLDKKASSEGSAAAGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGMDGGMSIWDVRSLESALKDLKIV

Entity 4 polymer

描述 description	Arp2/3 Complex 34Kda Subunit
分子量 formula_weight	34402.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

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

MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSISLKFYKELQAHGADELLKRVYGSYLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNCFASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKVFMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNASARDNTINLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTITGKTFSSR

Entity 5 polymer

描述 description	Arp2/3 Complex 21Kda Subunit
分子量 formula_weight	20572.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

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

MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ

Entity 6 polymer

描述 description	Arp2/3 Complex 20Kda Subunit
分子量 formula_weight	19697.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

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

MTATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEKVLIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITNFHTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKNF

Entity 7 polymer

描述 description	Arp2/3 Complex 16kDa Subunit
分子量 formula_weight	16295.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

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

MSKNTVSSARFRKVDVDEYDENKFVDEDDGGDGQAGPDEGEVDSCLRQGNMTAALQAALKNPPINTKSQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDNSSAVLLQWHEKALAAGGVGSIVRVLTARKTV

Entity 8 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 9 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 10 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	314

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6. 折叠分类 (SCOP + CATH) 21 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d1u2va1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.1 — Actin/HSP70

结构域编号 domain_id	d1u2va2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.1 — Actin/HSP70

结构域编号 domain_id	d1u2vb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.1 — Actin/HSP70

结构域编号 domain_id	d1u2vc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.4 — WD40 repeat-like
家族 Family family	b.69.4.1 — WD40-repeat

结构域编号 domain_id	d1u2vd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.198 — Secretion chaperone-like
超家族 Superfamily superfamily	d.198.2 — Arp2/3 complex subunits
家族 Family family	d.198.2.1 — Arp2/3 complex subunits

结构域编号 domain_id	d1u2vd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.198 — Secretion chaperone-like
超家族 Superfamily superfamily	d.198.2 — Arp2/3 complex subunits
家族 Family family	d.198.2.1 — Arp2/3 complex subunits

结构域编号 domain_id	d1u2ve_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.148 — Arp2/3 complex 21 kDa subunit ARPC3
超家族 Superfamily superfamily	a.148.1 — Arp2/3 complex 21 kDa subunit ARPC3
家族 Family family	a.148.1.1 — Arp2/3 complex 21 kDa subunit ARPC3

结构域编号 domain_id	d1u2vf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.198 — Secretion chaperone-like
超家族 Superfamily superfamily	d.198.2 — Arp2/3 complex subunits
家族 Family family	d.198.2.1 — Arp2/3 complex subunits

结构域编号 domain_id	d1u2vg_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.118 — alpha-alpha superhelix
超家族 Superfamily superfamily	a.118.13 — Arp2/3 complex 16 kDa subunit ARPC5
家族 Family family	a.118.13.1 — Arp2/3 complex 16 kDa subunit ARPC5

CATH v4.4 (12 domains)

结构域编号 domain_id	1u2vA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	1u2vA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	36 — Actin; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	70 — Actin; Chain A, domain 2

结构域编号 domain_id	1u2vA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	1u2vA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	640 — Actin; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	10 — ATPase, substrate binding domain, subdomain 4

结构域编号 domain_id	1u2vB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	1u2vB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	640 — Actin; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	10 — ATPase, substrate binding domain, subdomain 4

结构域编号 domain_id	1u2vC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	1u2vD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1460 — Yope Regulator; Chain: A,
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1u2vD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1460 — Yope Regulator; Chain: A,
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1u2vE00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1760 — Arp2/3 complex 21 kDa subunit ARPC3
同源超家族 H-superfamily homologous superfamily	10 — Actin-related protein 2/3 complex subunit 3

结构域编号 domain_id	1u2vF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1460 — Yope Regulator; Chain: A,
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1u2vG00
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	190 — Actin-related protein 2/3 complex subunit 5

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7. 引用文献 (1)

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晶胞边长 a length_a	111.300 Å
晶胞边长 b length_b	129.300 Å
晶胞边长 c length_c	204.700 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 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.550 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2250
R_work r_work	0.2230
R_free r_free	0.2580

fit	/app/data/saxs_computation/u2/1u2v/1u2v.fit
pddf	/app/data/pr_computation/u2/1u2v/1u2v.pr.out
profile	/app/data/saxs_computation/u2/1u2v/1u2v.dat

Crystal structure of Arp2/3 complex with bound ADP and calcium

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 (10)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. 折叠分类 (SCOP + CATH) 21 domains

SCOP 2.08 (9 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)