SAXSdb — 8glm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8glm
沉积日期 deposition_date	2023-03-22
结构标题 title	The Type 9 Secretion System in vivo assembled, RemZ substrate bound complex - conformation 1
关键词 keywords	T9SS, Type IX Secretion System Translocon, Protein Secretion PorV - SprA - PPI - RemZ Complex, MEMBRANE PROTEIN; MEMBRANE 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	43.99 Å
回转半径 Rg (电子) rg_electron	43.52 Å
零角强度 I(0) i0	1416230000.00
分子量 molecular_weight	309960.0 kDa
排除体积 excluded_volume	386520 Å³
包络体积 envelope_volume	522300 Å³
水化壳体积 shell_volume	94947 Å³
包络直径 envelope_diameter	154.6 Å
壳层 Rg shell_rg	52.56 Å
包络 Rg envelope_rg	42.69 Å
形状 Rg shape_rg	43.53 Å
总 Rg total_rg	43.85 Å
总原子数 total_atoms	21902
残基数 n_residues	2761
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	140.6 Å
Rg (实空间) rg_real	43.70 Å
Rg 误差 (实空间) rg_real_error	1.03 Å
I(0) (实空间) i0_real	1.4160e+09
I(0) 误差 (实空间) i0_real_error	2.6040e+07
Rg (倒空间) rg_reciprocal	43.99 Å
I(0) (倒空间) i0_reciprocal	1417000000.0000
解质量估计 total_estimate	0.8860
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	58.6 Å
偏度 Skewness skewness	0.087
峰度 Kurtosis kurtosis	-0.462
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	290600000.0000
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: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.963

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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 (5)

Entity 1 polymer

描述 description	Protein involved in gliding motility SprA
分子量 formula_weight	270221.7 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	A
原子数 atom_count	21902

MRKICIFLLVLFCGNVLRSQVKPAVQDTTKTQFSVGKMELENPPSILSAYKYDPITDRYIYTTSVDGFSIDYPLVLTPKEYEDLLLKESRRDYFRKKMDAIDGKKTGAEAAKKDLLPRYYINSSLFESIFGSNTIDVKPTGSVEMDLGVRYTKQDNPAFSPRNRSSLTFDFDQRISMSLMGKIGTRLEVNANYDTQSTFAFQNLFKLAYTPSEDDIIQKVEVGNVSMPLNSTLIRGAQSLFGVKTQLQFGRTTITGVFSEQKSQTKSVVAENGGTVQNFDLYALDYDNDRHFFLSQYFRNKYDVSLKNYPFIDSRVQITRLEVWVTNKQNRVTTTGGGNNLRNIIALQDLGEAQVSGVPDNEVVVISSTAGFFNNPIDSPTSNTNNKYDPATIGQAGSFLNSNIREIVTAKSGFNNTNVSEATDYSVLENARKLTTNEYTFNPQLGYISLQQRLANDEILAVAFEYTVGGKVYQVGEFGSDGVDATVVTGNNSSNQAIITQSLVLKMLKSNLTNVKNPVWNLMMKNVYQIPQAYQIKQDDFRLNILYTDPSPINYITPVQGSSFPPNPAPDSKVEQTPLLNVFNLDRLNYNNDPQAGGDGFFDYIPGVTVDVQNGRVIFTTKEPFGELIFNKLQTGAGESYNDPTTYNANQQKYVFRNMYRNTQAGALQDSDKNKFLLRGKYKSSGSNGIPIGAFNVPQGSVVVTAAGRVLVEGIDYSVDYQLGRVQILDPSLQASNTPIEVSLENNSIFGQQTRRFMGFNIEHKISDKFVIGGTYLKMTERPFTQKSTYGQESVNNTIFGFNGNYSTEVPFLTRLANKLPNIDTDVPSNLSIRGEVAFLRPDAPKASDFQGEATIYVDDFEGSQSTIDMRSAYAWSLASTPFITSINDNTFNANSNTLEYGFKRAKLSWYTIDPVFYSSKPSGISNDDLSLNTTRRIYSRELYPNTDIAQGQIQVVNTLDLTYYPGERGPYNNNPSFGASNPSANFGGIMRALNSTNFEQGNVEYIQFWVLDPYVGNGESPATNAGKIYFNLGEISEDVLKDGRKQYENGLGPDQVMVNPQPLWGDVPASQSLIYAFDTNPDNRKNQDVGLDGLPSSREGSIYTNYAGEADPAGDDYTYYLNADGGVLERYKNYNGTEGNSAVSINDPNRGSTTLPDVEDINRDNTMSTINAYYEYSIDVKPGMQVGENYITDIREVTNVDLPNGGTTNARWIQFKIPVSQPQNTIGNITDFRSIRFMRMFMTGFNSQMTVRFGALDLVRGEWRRYTGTLDANDQNPDDDGVEFDVAAVNIQENGTKCPVNYVMPPGVQREQLYNNNTVINQNEQALAVRIGGAGLQYQDSRAVFKNVSVDMRQYKKLKMFLHAESLPNQPTLEDDEMVGFIRFGNDFTQNFYQVEIPLKVTKTGGSCSISPDLVWMDDNSIDLALDLLTRMKIKAMSIDINSSKRDVNGIYYPDNDPDLEGGDGDGKLTLGIKGNPNFGLVRNLMVGVKSRADHKDIKGEVWFNELRLADLENKGGMAAILNVDTNMADFATVSATGRKSTIGFGSLEQGANERDREDVQQYNIVTNLNLGKLLPKKWGINLPFNYAIGEEVITPEYDPFNQDIKLDQLIRETTDQAEKDNIRTRAIDYTKRKSINFIGVRKDRAPEQKPHVYDIENFTFSQSYNQVERHDYEVADYEDEQSNSAVNYAYTFQPKEVVPFKSTKFMKKSEYWKLLSDFNFNYLPSNISFNTNILRQSNRQQFREVEVEGIGLDPLYRRNFAFNYQYGFGFNLTKSLKLNYSATSNNIVRNFLNDDNSPKEDFNIWDDYLDIGTPNQHAQQLVLNYDIPINKIPIFGFVKASYSYTADYMWQRSSTAFSEYEDPNGTVYDLGNTIQNSNSNTLTTTLNMNTLYKYLGLTPGAKKTAKPKTAAPPKPGEKIVNTAKPVVSSSPFYDGLIGVLTSIKNVQINYTKNSGTVLPGYTPSVGFLGTSKPSLGFVFGSQDDVRYEAAKRGWLTTYQDFNQSFTQVSNKLLKVTANIDLLPDLKVDLSMDRSYSENTSEQYSVDPSTNEYKPLSPYTYGMFSISTVMIKTAFSPSDETQSAAFDDFRSNRLIIANRLAEGHYGSGVAIPRYGDANNPIPAETDPNYAVYTANQGYPIGYTKSNQAVLLPAFLAAYTGSDASSSSTNIFRSFPIPNWSIKYNGLMRYKYFKDKFKRFSLQHNYRASYTINQFRSNFDYNSSPKVQDVNTNFYNEIIMSNVNLVEQFSPLIRMDFELKSSLRVLSEIKKDRALSMSFDNNLLTEVKGMEYIIGLGYRFKDVIFSSRLADNPTGIIKSDINIKADFSLRNNETLVRYLDYDNNQLAAGQNIWSLKLTADYSFSKNLTAIFYYDHSFSKAVISTSFPLTNIRSGFTLRYNFGN

Entity 2 polymer

描述 description	Peptidyl-prolyl cis-trans isomerase
分子量 formula_weight	19219.1 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

MKQLLTALLSLTLFISCSKDKDEVKDYTAENEKEIVDYLAQNNLTAQRTNSGLYYIITKEGSSESEGENPGEEENTGEGENTEENENDGHPTLNSNITVIYKGYFTNGKVFDESTEGVSYSLRTLIPGWKEGIPLLKSGGEIQLFVPAHLGYGSNGNKTVPGGAVLIFEITLVSVN

Entity 3 polymer

描述 description	Type IX secretion system protein PorV domain-containing protein
分子量 formula_weight	44210.0 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

MKKISLLLICLLITTFAKAQDIERPITTGVPFLLVAADARAAGLGDQGVATSSDVFSQQWNPAKYAFAEDAQGLSISYTPYLTDLANDISLGQVTYYNKINDRSAFAGSFRYFGFGGIELRQTGDPNEPTREVNPNEFALDGSYSLKLSETFSMAVAARYIRSNLKVATEEIDASAAGSFAVDVAGFYQSEEIAYSDFNGRWRAGFNIQNLGPKISYDHDDLSANFLPANLRVGGGFDFIFDDYNKLGVSLELTKLLVPTPPGPGTPYDANGDGDFTDPGDISQSQADEANYKKYKDIGWVSGIFKSFGDAPGGFSEELKEITYSAAAEYMYQDAFAMRLGYYHESPMKGAKQFFSLGAGFKYSMIKVDVSYLFSASKVKNPLENTLRFSLTFNFGDKYETY

Entity 4 polymer

描述 description	RemZ
分子量 formula_weight	113146.0 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

MDVQAWGGGGAGGGASGAVLDGRAAAGGGGGAYARSNITVAAGATLNASVAGTTTNALVSGAAVNGAAGGSSTILGFETSILALGGGGGGANNAGGTPAGGAGGSAASSVGNVSKLDGAAGGNGVTGAIGLLTVSGAGGTAGGGGGAGGAGVASVALGNGPGNAGTAPGGGGSGAMQSLLGGAQIGGSGAAGRVIITYTCPTYSITGISAANVCNSVGTTSVVTLTSSGGGLPIGPYVVTYNRSNPSGTGLTAIMNVTTPGTGTFTAAGLNVIGTSNITVTNLTSAACSSNISTNNVASLTVFAATVGGTLAGTATVCSGATSGTLTLSGQTGSIIKWESSVSPFTVWTTIPNTTNTYTSGALTETSQFRAVIQNGNCAVVNSSIATITVNPLPQGSLSANGPFCVTGSGQLTFTATAGTGPYTIVYKENGGADRTAANISSGVAFPTFTTPVTTTTVYTLVSVTGANTCSRSSGFTNNTATITVNSRIATPGFGTVTQPDCVTSTGSVVLTGLPAGSWTITQSGTASQTYNSSGTTYTISNLAVGNYTFTVQDAANCPSLATSTLTLIAPVVNIWNGTSWSKGSPPISTDVVRFSGNYSTTGNLSGCSLIVDSGFTVTVNSNHTLTISNAVTNNGGQLIFENNSSLLQTNNVTNVGNITYKRITPPVRRYDLTYWSSPITRTPPFTLYDLSPGTLADKYYSYDPVAGWVISFNGTQQMVPGRGYVVRAPQTNDLNTGANYLGAFVGVPNNGPISVSLGTAEAFQLLGNPYPSAIYADQFIANNSANLYGTLYFWTHNSLPSSSTPGGAQYNYDNNDYAVYNLSGSIIVGGMTGQGATTPGNQSAPLGYIAAGQGFFVVSKTAGNAVFTNSMRVAANNTQFYKTNKSAIERHRVWINLTNTQGAFKQLLIGYIEGATNFWDHNYDAITADANPHLDFYSINEGQNLVIQGRSLPFNESDVVPLGYRSAIAGEFSISLDHADGDLTNHAVYLEDKLTNTLHNLQTSNYTFNTAIGTFSDRFVIRYTTATLGTDDFENQTNSFYVSVKDKTIKLNSTEDVMREVSIFDISGKLLYNNKKVENTEFQVSNFQSGNQVLIVKVTLDNGNIITKKIVFN

Entity 5 non-polymer

描述 description	Lauryl Maltose Neopentyl Glycol
分子量 formula_weight	1005.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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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	2.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	422344

fit	/app/data/saxs_computation/gl/8glm/8glm.fit
pddf	/app/data/pr_computation/gl/8glm/8glm.pr.out
profile	/app/data/saxs_computation/gl/8glm/8glm.dat

The Type 9 Secretion System in vivo assembled, RemZ substrate bound complex - conformation 1

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 (5)

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 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)