9dei

Trypanosoma brucei mitochondrial RNA-editing catalytic complex 1, U-deletion (RECC1)

Method: ELECTRON MICROSCOPY D_max: 231.7 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	9dei
沉积日期 deposition_date	2024-08-29
结构标题 title	Trypanosoma brucei mitochondrial RNA-editing catalytic complex 1, U-deletion (RECC1)
关键词 keywords	RNA editing, tRNA, OB-fold, mitochondria, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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	65.76 Å
回转半径 Rg (电子) rg_electron	66.29 Å
零角强度 I(0) i0	2511540000.00
分子量 molecular_weight	396670.0 kDa
排除体积 excluded_volume	486830 Å³
包络体积 envelope_volume	779860 Å³
水化壳体积 shell_volume	105560 Å³
包络直径 envelope_diameter	218.1 Å
壳层 Rg shell_rg	57.67 Å
包络 Rg envelope_rg	65.54 Å
形状 Rg shape_rg	66.30 Å
总 Rg total_rg	66.09 Å
总原子数 total_atoms	27753
残基数 n_residues	3381
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	231.7 Å
Rg (实空间) rg_real	66.09 Å
Rg 误差 (实空间) rg_real_error	2.79 Å
I(0) (实空间) i0_real	2.5120e+09
I(0) 误差 (实空间) i0_real_error	5.0460e+07
Rg (倒空间) rg_reciprocal	65.40 Å
I(0) (倒空间) i0_reciprocal	2508000000.0000
解质量估计 total_estimate	0.8009
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	77.2 Å
偏度 Skewness skewness	0.334
峰度 Kurtosis kurtosis	-0.578
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0007
最高正则化参数 α highest_alpha	119500000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; 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 (15)

Entity 1 polymer

描述 description	KREPB5; RNA-editing catalytic complex core protein, B5
分子量 formula_weight	43818.9 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	28120

MRRAVVLHTAAPMCALTGKCVEDWESHRKSFDMRIFELLKGRVTSPTEPLPIKQIYATIANPCRLVEEFTCAKTTRRLGRLHTALSFLRRHNVLLHSLLFHVKETQTWNTTPDFDRLALYGESSLRHEVRARTLRLFPGIDSETYAALTSSVLSEEALHGLFDRLLMKALVGEKPVGKMRDWSLTPNQCGQMLCAIVGEMSWFAARTKATDRTHNNALFPPSDALILHVLCCHVLESLPAELLYNVLEPKVQRIKENWVNEPMSIPEQLHLKPRTIGSLSLSLVAKPLTEEEGRRKEVAVSAEKCQLSLTPERVIGSVRSTMLPRWNYKRFEERRYHILESDKRQVLPLAMSPVGRGDVSLASEQMPDERRRELVALALGGRYR

Entity 2 polymer

描述 description	KREPB8; RNA editing catalytic complex core protein, B8
分子量 formula_weight	41881.1 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

MHRGPPALLHNVGVATRSKSFAASTKLPGRLTPLPSTSSTLQPTNTLLSSSAGIASLRQLVSASTLTSTSTSGKKRVGSLDAHCRLLSRGTSADSYMPMTSRSFDVFEGNNKQAWLDLKTGWCHLCQEPLGATMGVHIGDRDHTNLQYFLFLYAAHGRRWSSEEVLRSCLATAPTVHNYATRHTTWDHLHVMDDALRRAELEALLFHLTHPPQQALSHVLQGRSPLGFWYSGERMWKLRISRLVTQVFPPISAGMMTNFTQKCWGRSNGERMYDALRLQRIKAYYGWQPYESKEKKAFFVRQLLWELLSVEVRDEVDELTKHMADLALRRMAFEMIFLQSMEYMHKVQYVYDLMGRPTVDELAAMNLL

Entity 3 polymer

描述 description	MP90
分子量 formula_weight	90093.0 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	C

MGLHWPLARSSNWCHMRALSNEHLRRRVGAAVRSIASTAPCFALERVEVAHSHAYSRRGVTVGFTSSSSSPSGKTGSGGLSPASQSLHSSSSFDASNGDVLANYVNFVADDATGPAATKENGAQPMRSLRSASAVENLLFTDAAKNYCRLCMEEVQVTPKAHISTPYRGSHTNHTCREVVLDSLALLAIRGYPIDDVYFVWADTLYQSSVFQRIPELVSPRWTVDKRSEVLAKILFMLKDMGVIDISLAAQAPDLFDNTAQQVHHRRRVAFERLEYIGDNSWGNHLSNRMMLLFPDRQWTYSQNAYTFNCFRDACEMNVTLEFMFDTLRVGELLPPGVREKLGTGKIKADVVEAVIGELHVTLWGLEPQLYDSVCFVEINGVGEARLAALVQHCLTEIYDLIVLSYVQELSGSAVPLAKQIAADRIWNSVYPPVRKAKDRAPGGRKSRSTVVNVVGVGEVRQLPSLPSLFPAASKRPTRAPHPLRRLRKLGEIPEETVCAGTNKDVFVHLIESYERLDMLDDSLLPTLNMRRLQDVQFSKLKRQLVPSLSPAALEELHNCKELDAESVTPHKVGDKEVATDERVLDLEEVYFRDKYFDLFPTPLPNEVVTKEGDCDKRQSGASTSRAVIISLPRGFDGSRPCNRAQLHMARNTIYPSLTERPAHSPTAGITKGDRVCLFSLSVYVPPDTKRPSAGVVTDKNLHFGEFAFHGVRIKGIECASEPECISRRSNAPGSDVGTSLNRSSWKEGGDNSCGTLTVEDGTGENSVVGEDGDTGVNGGEGKAEDATGKHLLRAKWCRENPFFPRASLPLLGISVGA

Entity 4 polymer

描述 description	RNA editing complex protein MP46
分子量 formula_weight	46525.1 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

MLRVENLRRSMTRLARHSLIRAVPFSPLSVGSSTDQTFGAPTRTPFRSHTCLLCDVSYESWGDHAESTTHIARHAICRTFVSPERHNAVMQQLWKHIRLDFGYVDEVTHKKEDRRRMRLASTMRHLQEKGVLHHSLPRVTVDAQSEVSLTVESDSFVNYMFLGESFARQETLDRVARLMPRAEALELSSIISFVLSKRRLAHFFDIFDMRKMVLNGDSSDDKASADGDVPPTIPRLQQDGKAVILFSCLGELQMFSRRDRSHSVATRSAAEQLVLNVLGTHVMENIIGELVHEALQTVVEEGTAVWREHCGELKHKLFEGTKAASPPIATTPNPVSNSGGPEVTADVNDQMWVDLCRLYVLDKNGSVPQLQPTVKRHSWHDVARALTLELTVPNPVNKSAVFAAAAPRLATKKK

Entity 5 polymer

描述 description	MP18 RNA editing complex protein, putative
分子量 formula_weight	18097.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,H,J,M,P

MLALTSRRLLLQQTFMRCCKSVNSVTLVGVVHDIQSGFVYEDAVTQFTLTTTSIDTTHPTQEVVVEKDHHTIRCFGELFSAEVKQKVKEGNVVCVNGRLRLSPQLEPSCNKHFYFPYIQVQPPHGQVAVIHGDRRTVPAAVNPAVEDIKSEKEGAGGDQSGVPS

Entity 6 polymer

描述 description	RNA-editing complex protein MP42
分子量 formula_weight	42318.5 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	F,N

MKRVTSHISRFLPLVLSQRGLSTYASPHVSSMRYYGATKCLLASTPDTPSFQCGECGKAFRLINALNHHIMTKHAGKAKAMMNKGGKLEEVNPEEIKNKPQGAMSQPTSPPPSSSTSGTEAASTSPTHSSFPGIPFSPVGGIGLVGTPVGAASHVVNTTTTAANSASGNALSDENADKKTFVCTICQKTFRLEAALQHHYQAKHNMEMPTSSSSSGGASAQPVLQGGATTAGVGSVGFSHTEEETGRSAMGTQYVHSQETILPQAPQYHLDVAPNAPEEGEVAAHWRCVNHCVMLGVVQNIQEGFVFEDKVLQFTLITDFEGPSPGDPDKDFHTVRVFDSDYSSRVKEQLRDGEWFLVTGRLRMVPQYDGSMRKYYHYPVIQVHPGCGSVLKV

Entity 7 polymer

描述 description	KREPA2
分子量 formula_weight	62983.0 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	G,K

MYRRFFRSAAVKHLGTTSAQCLMRATKYPCGAMCRNASSCHPQTLGYQQRFQSTTDKKFHCSVCKKPFRLEMAAKLHLQQAHGGDGSVEAGPGPGVEASSVNVVSTPVPSPISPVERTFVDEEERRPRRMRPTPKPLHQPDRDIPAAAMEEMLGVWDKIGLNRLEGNFVHSTMVMKVFAAPPDVSEIPLYEHVAPEGENPFDSLDHMTTGTVDATYVGHDAFAEVDLVDPFVAAPDQTLNPFRAGKVRNPFTRISPTQREVVKPLQPPQPKEEPLKAPVTPFGQLPMFGQTREPSASFAAAAVSVQAAANPNEVSSPFAAAVSSSPFVGQVASPFAPAQDVAGSPFEASPCAASSPFVTAGGQETSPFAAPSTPASFGQGSLFPPMGTGAPGFTAITETEQRQQELEHGCPTCGKKFSTFEGAAMHSKSKHGIVLESKKVKDRLNRKGVPDLPAYVPSPVDLSSTSPFGTRSAIGASWAETELIPHAQCVSNITIVGRVLDVSQASENVSHVTVFVEGERSGEEETLTLCCFGEVSQKIRGTLKRNATIFASGTLRLHPVYEASNNKYYVSPVVHVSMPTGTLAVIT

Entity 8 polymer

描述 description	RNA editing complex protein
分子量 formula_weight	23769.1 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	I

MWVRSLLLCIRRDPLQRAVDVAYASGMLLGSGSSRGTTHFSETTAFTSSNFAADLRGGRVGLAGDGGTKCEDRNGELVRGRIQFASRCAEGPFVGASPTVTSCAHIEGVVRQVECGYVGGDRVLQFIIEVEEVPASGGTPMRLPLAVRWRPGSEVAQNRMDEWQKEMERLVGRRVLASGRLQVEECFDSGSRRLYKTPSLVLPATSTVEMISLQELEC

Entity 9 polymer

描述 description	KREPA5
分子量 formula_weight	19081.9 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	L

MFSSTFRRLAIRPLNRVTMVGAMHDIQVGFLDRCSVFQFTLTCTVLDFQKVAEPQPKSPGSLPSSTRTAPNANGEEVEKHINKEQYTVRCLGSEAYTEALKNYLDDGCIVRVIGRLKTTEVVDAGKKQPFPCIIVEQGRWSTVSLVHSLRKQRRDWQLQNILTSVATLE

Entity 10 polymer

描述 description	RNA-editing complex protein MP81
分子量 formula_weight	81307.2 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	O

MRRLTRRSDRLCGKGNGGSCLQMSPTHVGAVVTWSLNRLMPLHTRTIPLRCSLPTPESGTTEPRELCFYETFELTGEDVHYLLLHEAHVKHGVLLNVPPQLAPNGTPPEVPEVIMPAAQLERMGGMKLAYEPTHLPPPLHTTGARQLVLDESFYTTPTKEKKATTTAVSHVSESTAASGGRGGASATAAGTALPPRLPPDPTMKFHCSACGKAFRLKFSADHHVKLNHGSDPKAAVVDGPGEGGLLGGAVTITTAKVAKHSSSAASGTASRAGDSATLDVKQQPDPQKELSASGISAVKIPYSKAVLSLPDDELVDELLIDVWDAVAAQRDDVPKSNSANIFLPFASVVTGTADRRKEMEAVARPTARATPEGAAPGIKRPGAMAGGAVAVGKGRSGGQILPIRELIKKYPNPFGDSPNAAVQDLENEPLNPFLPEEELAAQLQVACEEDTVVTPSACTTDVSTGSVIGKKGSLEKLKEKLRGTRPSMAASAAKRRFTCPICVEKQQTLQQQQSENVGSGFCTDIPSFRLLDALLDHVESVHGEELTEDQLRELYAKQRQSTLYPQKSSTGDGAGSRETPDDSEKKEGSVGNTSMDELKSLPEEVRRVVPPAPVEQDALAVHIRAGSNALMIGRIADVQHGFLGAMTVTQYVLEVDGDERINSKGVTTPASACTPDPASTKAVEAKGEEGEVVEPEKEFIVIRCMGDNFPASLLKDQVKLGSRVLVQGTLRMNRHVDDVSKRLHAYPFIQVVPPLGYVKVVG

Entity 11 polymer

描述 description	tRNA-valine (anticodon AAC)
分子量 formula_weight	24480.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	R

CGCUGAUGGUCUAGGUGGUUAUGACGUCGCUUUAACACGGCGAAGGUCUCGGGUUCGAGUCCCGAUCGGCGUACCA

Entity 12 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	5

Entity 13 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 14 non-polymer

描述 description	GUANOSINE-5'-MONOPHOSPHATE
分子量 formula_weight	363.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 15 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	367

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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	2.99 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	452724

fit	/app/data/saxs_computation/de/9dei/9dei.fit
pddf	/app/data/pr_computation/de/9dei/9dei.pr.out
profile	/app/data/saxs_computation/de/9dei/9dei.dat

Trypanosoma brucei mitochondrial RNA-editing catalytic complex 1, U-deletion (RECC1)

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 (15)

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

Entity 13 non-polymer

Entity 14 non-polymer

Entity 15 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)