9k9w

structure of bundle-shaped PBS with short rod

Method: ELECTRON MICROSCOPY D_max: 354.1 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	9k9w
沉积日期 deposition_date	2024-10-28
结构标题 title	structure of bundle-shaped PBS with short rod
关键词 keywords	phycobilisome, light-harvesting complex, photosynthesis; PHOTOSYNTHESIS
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	— Å
回转半径 Rg (电子) rg_electron	133.70 Å
零角强度 I(0) i0	396930000000.00
分子量 molecular_weight	5437400.0 kDa
排除体积 excluded_volume	6818600 Å³
包络体积 envelope_volume	10579000 Å³
水化壳体积 shell_volume	638900 Å³
包络直径 envelope_diameter	436.9 Å
壳层 Rg shell_rg	131.20 Å
包络 Rg envelope_rg	129.70 Å
形状 Rg shape_rg	133.70 Å
总 Rg total_rg	133.70 Å
总原子数 total_atoms	382772
残基数 n_residues	48186
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	354.1 Å
Rg (实空间) rg_real	129.50 Å
Rg 误差 (实空间) rg_real_error	1.07 Å
I(0) (实空间) i0_real	3.8150e+11
I(0) 误差 (实空间) i0_real_error	8.4060e+09
Rg (倒空间) rg_reciprocal	132.70 Å
I(0) (倒空间) i0_reciprocal	393200000000.0000
解质量估计 total_estimate	0.9121
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	161.0 Å
偏度 Skewness skewness	0.153
峰度 Kurtosis kurtosis	-0.639
角度范围 angular_range	— – 0.0550 Å⁻¹
当前正则化参数 α current_alpha	0.6329
最高正则化参数 α highest_alpha	10710000000.0000
实空间数据点数 n_real_points	12
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.001; Oscil: 0.999; Stabil: 0.979; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.000

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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 (12)

Entity 1 polymer

描述 description	Allophycocyanin beta subunit
分子量 formula_weight	17241.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	42

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,Z,L5,N5,B5,D5,F5,H5,J5,d5,f5,P5,R5,T5,V5,X5,Z5,b5,P7,R7,B7,D7,F7,H7,J7,L7,N7,h7,j7,T7,V7,X7,Z7,b7,d7,f7,l7,n7,p7,r7,t7,v7
原子数 atom_count	382772

MQDAITAVINNYDVQGKYLDGAALDKLKAYFTTGAVRVRAAAVISSNATTIIKEAAAKALIYSDLTRPGGNMYTTRRYAACIRDMDYFLRYATYAMLAGDPSILDERVLNGLKETYNSLGVPIAATVGGIQAMKEVVGGLVGPDAAKEASIYFDYLSSGLS

Entity 2 polymer

描述 description	Phycocyanin alpha chain
分子量 formula_weight	17679.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	84

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	;AA,CA,EA,GA,IA,KA,OA,QA,SA,UA,WA,YA,O1,Q1,S1,A1,G3,I3,K3,G2,I2,K2,A3,C3,E3,A4,C4,O3,Q3,S3,U3,W3,Y3,T4,V4,E4,G4,I4,K4,N4,P4,R4,X4,C1,K6,A6,C6,E6,G6,I6,E1,A8,C8,E8,T8,V8,X8,G8,I8,K8,N8,P8,R8,O9,Q9,A9,C9,E9,G9,I9,K9,S9,U9,W9,Y9,G1,I1,K1,U1,W1,Y1,A2,C2,E2 ;

MKTVITEVIASADSQGRFLNNTELQAANGRFQRATASMEAARALTSNADSLVKGAVQEVYNKFPYLTQPGQMGYGDTNQAKCARDISHYLRFITYSLVAGGTGPLDDYIVAGLREVNRTFNLSPSWYIEALKHIKGKVGSQLSGQPLTEANAYIDYCINALS

Entity 3 polymer

描述 description	Phycocyanin beta chain
分子量 formula_weight	18479.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	84

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	;BA,DA,FA,HA,JA,LA,PA,RA,TA,VA,XA,ZA,P1,R1,H3,J3,H2,J2,L2,B3,D3,F3,Z3,B4,D4,L3,P3,R3,T3,V3,X3,B1,S4,U4,W4,F4,H4,J4,L4,O4,Q4,Y4,J6,L6,B6,D6,F6,H6,D1,B8,D8,U8,W8,F8,H8,J8,L8,O8,Q8,S8,F1,L9,P9,Y8,B9,D9,F9,H9,J9,R9,T9,V9,X9,Z9,H1,J1,L1,T1,V1,X1,Z1,B2,D2,F2 ;

MQDAFTKAIVAADLRGSFLSEQELNQLTNLVKESNKRLDAVNAITGNAAEIISDAAHKLFAEQTDLIRPGGNAYPNRRMAACLRDMEIILRYVSYALLAGDASVLEDRCLNGLKETYVALGTPTRSVARAVQLMKETAIGYVNSPSGVTRGDCSALVNEAATYFDKAAASIA

Entity 4 polymer

描述 description	Phycocyanin-associated rod linker protein
分子量 formula_weight	30913.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	MA,M3,M4,M8,M9,M1

MNVLTTSSQRGGKLFKVTMTLSPALSHHPWPSLDTYEPSQNSYSVVVPLDRLLAEMTYIKNKGGRVLDISPADLEALGPPDISSVAIPLKVELWAKADVSDVQAAIVAAYKQIFGNTYVLESERLTSAESLLRNGSISVREFVRLLAKSELYKERFFFCTSNNRFTELNFKHFLGRAPYNQSEIAAHLDRYQTFGYDAEIDSYIDSDEYIQAFGENVVPYYRGFKSQSGQTVESFNRMFKLYRGDAGSDTNLNLQGQKRRVDPKNLLRSGRGIV

Entity 5 polymer

描述 description	Phycocyanin-associated rod linker protein
分子量 formula_weight	31085.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	NA,N3,Z4,N9,Z8,N1

MSVLTGDNQQRGSKLFKITIALSPTLAHHPWPGLDTHEPSQSSYSTIVSLERLLPEMTRIKRNGGRILEITEGEASESRANFPAVMEPPVVELYPRAGEAEVQAVIAVAYKQVFGNIHVMESERIVSAESLLRNRSISVREFVRLLAKSDLYKESFFHCTSNNRFIELNFKHLLGRAPYNHSEIIEHLDRYQSQGYDAEIDSYIDSDEYVKTFGENVVPYHRGFKSQVGQQSVAAFERMIRLFGGDASSDTSLNRTGQKRLVDPKQLLRSGRGIV

Entity 6 polymer

描述 description	Glr2806 protein
分子量 formula_weight	81544.3 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	M2,M6

MSATTYDWRKVIDSIKIEDPVKPGDFANFLDMARGIESRTGVWSISYESLRTLGPPEGGMLRPAVGGTAEAAAQKQLGITAVAPASVVELRPNASEEDLQGVLRAVYRQVLGNTYVMESERPTQAESLLRNGSISVREFVRRIAKSDLYKERFFNKASNNRFIELNFKHLLGRAPYNHGEIQEHFGLYHKAGYDVEIDSYIDSDEYIETFGENIVPYFRGFKYQTNQSAGGFPRMVKLWGGDAGSDTDRGKNGQRTLVTTKDLIGPTKIFVPFVAPGRDADMVSGDYTRLAFGLSGEAAAQRQLGIASVAPAPICQLRPNASEEDLQGVLRAVYRQVLGNTYVMESERPTQAESLLRNGSISVREFVRRIAKSDLYKERFFNKASNNRFIELNFKHLLGRAPYNHGEIQEHFGLYHKAGYDVEIDSYIDSDEYIETFGENIVPYFRGFKYQTNQSAGGFPRMVKLWGGDAGSDTDRATGGQRTLVTTRELVKTLPLLTEIPAVPATRGFEQVLNQLKRPAPGGTGEAQGQKQLGITAVAPAPICQLRPNASEEDLQGVLRAVYRQVLGNTYVMESERPTQAESLLRNGSISVREFVRRIAKSDLYKERFFNKASNNRFIELNFKHLLGRAPYNHGEIQEHFGLYHKAGYDAEIDSYIDSDEYLLTFGEDVVPYFRGFKYQTNQSAGGFPRFTKLYGGDAGSDTDRGKNGQRTLVTTKDLVVSGQFSKPV

Entity 7 polymer

描述 description	CpcD protein
分子量 formula_weight	7776.9 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	N2,N6

MYNNVTANTEWGRKVFKITVAQFPDADGLDTDNLSQSNYFVTVPLARLLPEMQLIKNKGGKVLSVEPVVS

Entity 8 polymer

描述 description	Allophycocyanin alpha subunit
分子量 formula_weight	17539.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	40

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	K5,M5,O5,A5,C5,E5,G5,I5,c5,e5,Q5,S5,U5,W5,Y5,a5,A7,O7,Q7,S7,C7,E7,G7,I7,K7,M7,g7,i7,k7,U7,W7,Y7,a7,c7,e7,m7,o7,q7,s7,u7

MSVLTKAIVNADAEARYLSPGELDRIKSFVASGERRLRIAQTLTEARERIVKQAGDQLFQIRPDVVSPGGNAYGEKMTALCLRDLDYYLRLVTYGIVAGDVTPIEEIGIIGVKEMYNSLQTPIPAVAEGVRAMKNVATSLLSGDDAAEAGFYFDYLVGAMQ

Entity 9 polymer

描述 description	Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
分子量 formula_weight	7633.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	z5,i5,z7,w7,x7,y7

SRYFKVTACIPSLKRVRTGRELQNTFFTKLVPYENWFTEQQRIQKAGGKVLSVKLFTGVQGANTGVGA

Entity 10 polymer

描述 description	Phycobiliprotein ApcE
分子量 formula_weight	130002.3 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	j5,k5

MSIRGTSGSTVARPRLFRTVMTETINGINAEDRYPNSGEVSQLDQFFGDGQRRIAIVAKLTENAEMIVSRAANRIFVGGSPMAYSERQKAKAKSPLANDEFGNEPIVEDRGGFLESLKSIFSTRGGGGRASADFAVPPDFEPINIARYGPERMQKSIRDLDWFLRYTTYAILAGDPSILEANCLGLREILEKSCSISATIVALLEMRKNAARLFKDEADSKLVSSYISVVIRALDADRSDAPADIVRPSSEDRPGLTLPYIYKLSADSLTTFKMTAIYGADGRPKVNLSSDEKERVVRAAYRQVFERDLKAYGQSVSEAESKVKNGEISVREFVRRLGKSELYRREFYQPFINSRVLELAFKHFLGRAPESRAEVQKYFSIISSPIVRGQSSMPSGGLYALIDALIDSEEYTSIFGEDTVPYLRNLGVEAQPSWNWGAAYDLYNYAAPRRKVPQFITLFADYTQPLPNQHPYGAGNDPLEIQFGAIFKNSTINPAERAAPIGKDVKRILIRNGSPTSNERGNPTGMSEGATTLGPKIFKLTQNVGFRSKGMVQNAGVVTVEGSVQALITAAYQQIFGRQLYQGQRLKVAEIKLENGETTVKEFVRALGRSEIFRKLYWEPFYVCKAIEYIHRRLLGRPTYDRVENNRYFDIASKKGFYGVVDAMLNSNEYQEVFGEDVLPYERYLTPAGLSLRKGRFGSSDVLTTPGGITPRGDAARMMDKIQELGTPINERSIPEMYVNQGVPALKRQRKVFKQSQATDRESFDALVTAAYVQVFDKDIASYIRSEFSALESRLRNRETSVKEFVRLLGFSALYRKQFHDRYPNTKVVEFAFKHFLGRAVKNQAELIKYHGLLGRKGIKALIGALVDGEEYGRLYGEDTVPSWQFPTLPAANYPNSVELYNRFTRQDDSLVVPSFKPIRSKMDIASMPLVQAALKEQQATKTALDMSRPMFLELGRSFKGADGQSVEVGVGTLRRQLEHIYRIAPDATRSEKDVAINAIYRQVLDVFAGIPPSYLRLSEAESKLKNNEISVREFVRRLGRSENYRKRFFEPYSSPKVVELLTKHFLGRAPISQQEISTYVQILGTKGLAAAVDAIVESPEYLTIFNEDIVPYRRYPTLPAGNYRASVRVNDEELISQSWSSLSPTYTGYQYVTR

Entity 11 polymer

描述 description	Glr1262 protein
分子量 formula_weight	92127.6 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	a9,aA

MSTVLDDQSKAYAPGSANGPTAGLEPFVRMSRMIRSGVPEDREEPDELWLSMVRDIFGRGYMDRLSQTRAIDYSAFVRPADQATADGAAQTKLGITAIAPDQGVELRPNFTEADVITVIRAAYKQLFGNTYILESERVIQAESLLRNGSISVREFIRILAKSDLYKERFFRCTSNNRFIELNLKHLLGRAPYNQGEIAEHLDRYCQSGYDAEIDSYIDSDEYRRVFGENTVPYFRGFKYQVGQSAAAFERMRALYSGDAGSDTDRNQNGQRTELTSGLADPAQPVRARTDYALTRVDIPGGNGAAGRLAALDESLGSWLDAARDLISQNDYSQKAIEVEPKRVAPYAQYLTPAVEATPDAAAQTKLGITAVAPDQAVELRPNFGEAEVQAVIRAAYKQIFGNTYILEADRVVIAESLLRNGSISVREFVRLLAKSDLYRDRFFRTASNNRFIELNFKHFLGRAPYSQAEIGEHFNRYHKSGYDAEIDSYIDSDEYRRVFGENTVPYFRGFKYQVGQAARGFDQMQQLFAGDAGSDTDRGIGAQPAAKLTFPLSRPLGVTSAYFPSSQGGAATSDGLEMFTRMARELTVTPVSARRTTSPTAPTAPAMPLAGYYSRPAPRATADGDAQTKLGITAVAPAQAVELRPNFGETELQAVIRATYKQLFGNTYILEADRVVQAESLLRNGSINVREFVRLLAKSELYKERFFHCTSNNRFIELTFKHLLGRAPYNQSEFVEHLDRYQKSGYDAEIDSYIDSDEYRRVFGENTVPYFRGFKYQTGQAAGVFERTLKLYGGDADSDTNRNRQGQLRQVDPQELLRSGRGIV

Entity 12 non-polymer

描述 description	PHYCOCYANOBILIN
分子量 formula_weight	588.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	336

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7. 引用文献 (1)

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分辨率 resolution	2.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	389430

fit	/app/data/saxs_computation/k9/9k9w/9k9w.fit
pddf	/app/data/pr_computation/k9/9k9w/9k9w.pr.out
profile	/app/data/saxs_computation/k9/9k9w/9k9w.dat

structure of bundle-shaped PBS with short rod

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (12)

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 polymer

聚合体 Polymer

Entity 9 polymer

聚合体 Polymer

Entity 10 polymer

聚合体 Polymer

Entity 11 polymer

聚合体 Polymer

Entity 12 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)