SAXSdb — 8ghn

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8ghn
沉积日期 deposition_date	2023-03-10
结构标题 title	Composite model of the yeast Hir Complex with Asf1/H3/H4
关键词 keywords	Histone, Complex, Replication-Independent, CHAPERONE; CHAPERONE
实验方法 method	ELECTRON MICROSCOPY

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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	79.85 Å
回转半径 Rg (电子) rg_electron	80.00 Å
零角强度 I(0) i0	9352360000.00
分子量 molecular_weight	848140.0 kDa
排除体积 excluded_volume	1072100 Å³
包络体积 envelope_volume	1892500 Å³
水化壳体积 shell_volume	201410 Å³
包络直径 envelope_diameter	255.1 Å
壳层 Rg shell_rg	78.66 Å
包络 Rg envelope_rg	75.92 Å
形状 Rg shape_rg	80.04 Å
总 Rg total_rg	79.85 Å
总原子数 total_atoms	59784
残基数 n_residues	7401
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	217.7 Å
Rg (实空间) rg_real	78.27 Å
Rg 误差 (实空间) rg_real_error	0.76 Å
I(0) (实空间) i0_real	9.1850e+09
I(0) 误差 (实空间) i0_real_error	1.7540e+08
Rg (倒空间) rg_reciprocal	79.56 Å
I(0) (倒空间) i0_reciprocal	9345000000.0000
解质量估计 total_estimate	0.8914
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	98.0 Å
偏度 Skewness skewness	0.334
峰度 Kurtosis kurtosis	-0.272
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	0.1673
最高正则化参数 α highest_alpha	333000000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 0.989; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.683

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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 (7)

Entity 1 polymer

描述 description	Protein HIR1
分子量 formula_weight	93983.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,G
原子数 atom_count	59784

MKVVKFPWLAHREESRKYEIYTVDVSHDGKRLATGGLDGKIRIWSIDSILRCMELESLTPEIPLPQDLQMPLCSMSRHTGSITCVKFSPDGKYLASGSDDRILLIWALDEEQSSQPAFGSEHEREHWTVRKRLVAHDNDIQDICWAPDSSILVTVGLDRSVIVWNGSTFEKLKRFDVHQSLVKGVVFDPANKYFATTSDDRTMKIFRYHKTGDISFTIEHIITEPFKESPLTTYFRRPSWSPDGQHIAVPNATNGPVSSVAIVNRGTWDTNVSLIGHDAPTEVARFNPRLFERNAGVKQKKDDDPENALVGQNDDKVHHFDKNIDSVVATAGQDKSLAVWSTSRPRPILVAFDIANKSITDMSWNPDGSLLFVASLDSSITLFKFENNELGKPIPLEKNMEQLYRYGVDKDSLDFPESINQLLLEDQTKSFKHTKISTSKLGENHPTLATNSASNQKDNNDASVSRSEHINILIPKRKKDAILNKAVTLKSGKKRVAPTLISTSSSSPFSNGIKKPTLDSKRIENNVKSSTKTINSKNTLLNVPEGVEKKISISSFPLPRLGIHSLIMGTKERSAWKISNSELENDDADNAGGKGSDGTSNSIDDIAVLSEEENDFHRMTLNAKLTQEKIWSEEPTTRCLLQSDVIPDTDVVVLEGGSLDDIAVLEIRNGVERSIQFDSEALLDNPTRILGYQGGKRTIETFIPEVIICAIGSKDCKCWCLASANGSIYILSYNGQQRIPKICLGHKVIKMVTSSKYLLVLTERGLFFAWDLLDLKLVLRNVPILPILNGQPIHGNKVRINKVIKCFRLDGSSCDLLLEVGDPKNVYKWTKDLGCWSLYK

Entity 2 polymer

描述 description	Protein HIR2
分子量 formula_weight	98553.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,C,H,I

MRLLKYPLDIHNEQVNALAALGPYIILAGSGGHVMAWRQQQLVDTAFDRVMIKDLKPEVSFQVDQDTTGDIFFITGDLETLYIGSEHRLWGYSGWLCRDTNNINSVEKMNSKLLFECKSPSTITDVKYDINLGILFVLLSNENKILLFRHKTFDKLSEITIDKASKPITGIIDPTGQTFTVMTSDRSILVYQINKTGTHKLINKLTQHVQMYPLHYRISMSPQADILPVINSVKGVPNNATSCTALLDRNNNYKVTKTLVTPSSNGCRVLVYSPAFYEKPNLKKGTSTRYNLIATSGSTDGTILVWNTKRMKPLFNALQVSSTAINDMSWSQDGFTLFAISNDATLYTFAFQEKDLGVALPQTEIKSLQEVNKKLPKLEEPLAEQIPKSFPENIKLEESASAAPIPNDIGRSAVGKKPTKKKTANNQTNGIKTIQSTSMEFNTPSYTVPRDLKRKPKEATPSNIAPGSKKQKKELQPIDFLDTGLLLPNTSFSRIRLATPKIRSTFKYSPINNPNLILDVKNGSGNEQRPTIVKLTSKVLDQDQVLFQDFIPKLITICTAGDTFWSFCSEDGSIYIYSDSGRKLMAPLVLGVSISFLEACGTYLLCLTSIGELYCWNIEQKKLAFPTNTIYPLLNPSLRYSDDILTRAENITLCSITKKGVPLVTLSNGDGYLFDKNMETWLLVSDGWWAYGSQYWDTTNTTGLSSSKANTDSFNGSESNINEIVSDIKNDNQSIINFLECKTNDELNRKGRIKNLQRFARTILMKEGFENMEEIVTLSHLENKILISIRLEEPEEFSKLMMVYCIRLSELGYMDRLNDVFQWLYDDLPISGTGSAFADKDFKRNLLKKILIACGDIRQVQRVTTRYAKEMNIIS

Entity 3 polymer

描述 description	Histone transcription regulator 3
分子量 formula_weight	191915.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

MSMFNALNSNIEGEQYEAEEHSRELQIEQSFNILQDALIDLKNKDFEKSDSKFQELFQIDVVKPDRWGMYRNSSPTLDNLRYLCYRNRGMYYHLYLENNYERLNSQELVNCILKAVENLVESIQHSDADFAVTDLLARIFKSFNSVKLERLISEYEFTKQENLSLLLGRHRKFLLNDLTLMMNNYVELTNKLLVPNLSDNTIFERYHLEKYKDIKPEPLAFGPILSRISEMKKQDEEIMKKLDVFNVTLNEESWDEVAKALKNLLPSVKTSSLIGRNMDPYNEIEEPIEAVKFELSEAINNTPSLDRESERQEEEQDNESVRADDKSGNLAPSDIQTNEEARPNKRTDEHIDSTKPLQRSSKRFKEREQENSKELVMDVHKRFFGEFNTLLSYIHILPFCDFDTFASKFIIGSSDKQPEKFIPYTDLYECLKSWSSRYTDIFNQNDYLSSGSNENEELFQLNALLKSNAFDDKESFPRYLNDLDSDHIRSFISEVNAGNLHFHQVRLKLLFKLLGTYDEGNGRRLIIDYLWESQLLKIVLWFVFGIESNIFALINKNKRQCKYLALSIYELLVNHLGNIVEEITNKRIQGHKSADLKSQRNKVEKRIRSWHTLLEQIADEKDKELYVHFQWTHYCFLQYTCDIVDSRLSETLTSLENTIKDSDSSLDIAYPNYRHIPALNLNTVQSQKRKIRIIQNITVEDISEDTNSDTHSENHLETLEKVLLHILHPSTNHSNIDEEMVSFIFNSPFLLKIRLWGVLFSSYVKKSSIQDVQRIYFHVLDFMKGALTSPVYKESNPHGRHQMLLTVLTAIGYLSSQLTAILNSNRWESSDFVLEDYMFEKLLQTFFFFYTVLFYESSAVNDVSNKSFFKRASKSSGKMKDIMIDLATLILYYYDLQAKLRTPAEQGIETTELIWSLHTLFGHFHFCDASNGKFLDLAEKLLCQFINNDSFLQLKQILWCRYHYAIASDNFSPDLHDTKAVEMEKIHSLPLGTYLIKLQYQNKNPYLSSSKTTLKQIMDNIIEKIGDPSTLDNHIISRNSFLLNEYLSRPITADLLKHTFSGATSLYLTSPNDELQQGMTAGLFYVSSLQSLGLYKMRKKSMQARPSELDSIIRMLKNDIIYNTNRFESWILLGKCYSYIVEDDLIWTSDKITVPEKKDVIALTQRKAILCYLMAISIYYSKLDRTIDDKKIILEALDDLGSMLISGYYNPMNKLCFSWKSSAENTMRLSETGEVVMEKTKKITTISDFNIEQSIFLCFNRACSLSGDIKSQDDVFVLNWSSFYNLAKFFFKTDGGNNCKLVAKYITQGCQIAYESSPAKDPIIEPHYLLVNACYKWVKRGVIGVNEALTLLSKDNQFFQEQEEFWVNDEGLAWDYQEKFFFDKIIRLLRHLLSVDKKKWQHRPRYRIARILFDDLGDVNGALEEMDSLISAKSINKNLVNIWKPDFERPGKHFIYTYQYLVLYLDLLFAIKDFNTTGLVIKKLRRFGSGTVNVNELLERAINVYTQSAKIKLQLQDKSYVEQILPTLNYQEFLKISEQLNQVFDQGKYPEEISSGLKLAFQLKKGHSGIAFDSVCLGIYFEYLYFPLARQDQSLTDVNDENNPALPSSGSVTSKSTPDPTSKPSAIKKRVTKKEVFDRVRLLVDKIT

Entity 4 polymer

描述 description	Histone promoter control protein 2
分子量 formula_weight	67877.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

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

MDQKAIVLDNSKSGSKQTKSSGKMQTQTDTNAEVLNTDNSIKKETGSDSEDLFNKFSNKKTNRKIPNIAEELAKNRNYVKGASPSPIIISGSSSTSPSGPSSSSTNPMGIPTNRFNKNTVELYQHSPSPVMTTNKTDTEEKRQNNRNMDNKNTPERGSSSFAAKQLKISSLLTISSNEDSKTLHINDTNGNKNSNAASNNIPSAYAELHTEGNSIESLIKPPSSPRNKSLTPKVILPTQNMDGTIAKDPHLGDNTPGILIAKTSSPVNLDVESTAQSLGKFNKSTNSLKAALTKAPAEKVSLKRSISSVTNSDSNISSSKKPTSEKAKKSSSASAILPKPTTTKTSKKAASNSSDSTRKKNASNKTTSAIKKESNAGSKLNTVKKENSSLSSIKATEKEKDKGGNSTEAKNSTSNVRKEPTAKSPKRLVAAPTVSPPKILQTAETKAKEPSILIDVPLYQADTNDYLDENGQVIFNLSTLIKEKYHPKSKELAQLKDSKRNLLMQLSDHSNGSLEKEKDEEGDVIELDDDEDMEEDEGEIDTETNTVTTTISPKKKSHPMKGKNLIGKYDVEDPFIDDSELLWEEQRAATKDGFFVYFGPLIEKGHYASLERANGTMKRGGVKNK

Entity 5 polymer

描述 description	Histone H3
分子量 formula_weight	15391.0 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	M

MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQKKDIKLARRLRGERS

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 6 polymer

描述 description	Histone H4
分子量 formula_weight	11395.4 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	N

MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 7 polymer

描述 description	Histone chaperone
分子量 formula_weight	31629.3 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	O

MSIVSLLGIKVLNNPAKFTDPYEFEITFECLESLKHDLEWKLTYVGSSRSLDHDQELDSILVGPVPVGVNKFVFSADPPSAELIPASELVSVTVILLSCSYDGREFVRVGYYVNNEYDEEELRENPPAKVQVDHIVRNILAEKPRVTRFNIVWDNENEGDLYPPEQPGVDDEEEEDDEEEDDDEDDEDDEDDDQEDGEGEAEEAAEEEEEEEEKTEDNETNLEEEEEDIENSDGDEEEGEEEVGSVDKNEDGNDKKRRKIEGGSTDIESTPKDAARSTN

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

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

分辨率 resolution	2.96 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	639629

fit	/app/data/saxs_computation/gh/8ghn/8ghn.fit
pddf	/app/data/pr_computation/gh/8ghn/8ghn.pr.out
profile	/app/data/saxs_computation/gh/8ghn/8ghn.dat

Composite model of the yeast Hir Complex with Asf1/H3/H4

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (7)

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

来源 Source

Entity 6 polymer

聚合体 Polymer

来源 Source

Entity 7 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)