9n2d

Cryo-EM structure of an extended F. johnsoniae BAM complex, composite map

Method: ELECTRON MICROSCOPY D_max: 176.5 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	9n2d
沉积日期 deposition_date	2025-01-28
结构标题 title	Cryo-EM structure of an extended F. johnsoniae BAM complex, composite map
关键词 keywords	BAM complex, BamA, BamD, BamG, BamH, BamM, BamP, outer-membrane proteins, OMP, 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	54.72 Å
回转半径 Rg (电子) rg_electron	54.77 Å
零角强度 I(0) i0	942229000.00
分子量 molecular_weight	261570.0 kDa
排除体积 excluded_volume	329330 Å³
包络体积 envelope_volume	530520 Å³
水化壳体积 shell_volume	83050 Å³
包络直径 envelope_diameter	177.9 Å
壳层 Rg shell_rg	55.71 Å
包络 Rg envelope_rg	52.68 Å
形状 Rg shape_rg	54.75 Å
总 Rg total_rg	54.86 Å
总原子数 total_atoms	18464
残基数 n_residues	2284
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	176.5 Å
Rg (实空间) rg_real	54.80 Å
Rg 误差 (实空间) rg_real_error	1.71 Å
I(0) (实空间) i0_real	9.4220e+08
I(0) 误差 (实空间) i0_real_error	2.0710e+07
Rg (倒空间) rg_reciprocal	54.62 Å
I(0) (倒空间) i0_reciprocal	942000000.0000
解质量估计 total_estimate	0.8666
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	54.8 Å
偏度 Skewness skewness	0.265
峰度 Kurtosis kurtosis	-0.725
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	47710000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.457

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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	Bam D
分子量 formula_weight	30219.4 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
原子数 atom_count	18488

MKKIVSLLIVAALFCSCSEYQKALKNEDVAAKFEVATKMYDAGKYNKAIRLFEQLAPTYRGKPQAEKLFYMFSQSYYKTKQYYLAGYQFESFVSGYPRSEKVQEAAFLGAYSYSKLAPVYSLDQADTVKALDKLQAFIDNYPNSEYLAQANESVKILNGKLEKKAYENAKGYNTISDYKSALVAFDNFIADFPGTPLKEDALFYKYDSAYQLAINSVPSKMEERLHVAQTAYANLMKYKSDTKYKEKADQMNARVETDLQKFTK

Entity 2 polymer

描述 description	Bam A
分子量 formula_weight	101490.3 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	A

MLQKRIPQIICTLLLLGSFSQIKAQDRVPFDQGKKYTLAKVSVVGKISFNEQTVVTFSGLQKGQEITVPGEEITSAIKKLGKLGLFDEIAFYINKVENDSIYLDLNIVELPKLNEVKITGVKKSKVEGLIKDNNLTKNKIVNENLITTTKNYIENKYKKDGFYNTKVVITTTPDTTAGNQVNMLVRVDKGDKVKISSIDFTGNKQLSDSKLRAAMKDTKQKNVLRVFKASKFIPEKYKTDLEKVIASYKEKGYRDARIIYDSVIYNKKKNMLAIKIDVEEGNKYYFGNIKFLGNTVYSDQQLNRYLGIKKGETYNGVLLEKRIADNTKPDGEDITNLYQNNGYLFSKINAVEVKTVNDTIDFEIRITEGPIAYFNKIYVTGNDKTNDHVIYRELRTKPGNKYSKEELVRTIREIGQLGFFDPESIKPEFRNVDPAAGTVDIEYQLVEKGSSQVELQGGYGGGGFIGTLGLSFNNFSARKLFDKDAYKPLPMGDGQKVALRLQGSTYFQTYSLSFSEPWFGGKKPVQFSSSISYSKQFNYNYSSRDVNRNQSFNIFTVQVGLAKRLTVPDDYFVLSQSVSYQHYDLNNYYTGLFTFGNGASRNLAYTIGLSRSNKGVNPIFPTYGSEFSISAKVTPPYSLFNNINYGDLQNQKEYKTQYTGTTTTTGIDGQAINPGDYTKTETVNGQSGTVSVGSDYKSADTDVGKVDQKKYNWLEYYKVKFKADWYTKIYGKLVLRTLTEFGFLGAYDQSRGVVPFERFYLGGDGMANYSMDGRETIQLRGYPNNSLTPIIEDRNSSRYGQQIGATIYNKFSMELRYPITLKSSASIYALTFLEAGSSYPTFKDYNPFDLNRSAGAGLRVFMPAFGLLGIDFGYGFDALPGSTTNKANGWETHFIIGQQF

Entity 3 polymer

描述 description	Bam H
分子量 formula_weight	57094.2 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	C

CDKDFNAIGGDLIGDDHFGLESEKYDVLSYNQEVTSVQSNVLPTSALGIYSNPVFGETTANYVTQVALVAYAPSIGEDPVIESAVLSIPYFSHVTANNTDGSHTYELDSIYGPANGKLKLSVYESGYQMRSSFPSNGTELPQYYYTSQNSTFDQAKVGTRLNDDLTKPFQNDQFFFSSEEYKTVTKDSNDKETTTYTAPEMRLNLNSAFFQDKILKAPASKIASTDVFQEYFRGLYFKVEKADGSPSNMALMDFSKGKITITYKAKTDITTDAPETTEERTIVINLVNPTSSGGTANLLQDAKSAGYSGAISSSNVNKTEGDERLYIKGGQGSAAVIKLNDFASKLDDIRAKNWKVNEANLIFNIDSDLMTGADEPKRVYLYDLTNNVPLADYYADQTTSLTVGDTKGAKYVFGGLINLGDNKRGKTYKIRITEYIRNLIKDKTAKNVNLGLVVTESIGITTSNFLENRIVLQPNEYFSQVPRASIMNPLGTILYGGKASVPDDKRLRLEVYYTKPN

Entity 4 polymer

描述 description	Bam G
分子量 formula_weight	44459.0 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	B

MIKKIIISACLLISFVSFAQQGTASPYSFYGIGDIKFKGTLEYRSMAGVAVEQDSIHLNIENPASYASLMQTTFTVGGTFGTSTLKSNTGSAKAQRTTFDYLAVGIPVGKFGVSFGLIPLSSVGYKILDDNTATEGAVSSQLSGKGGINKVYFGVGYKIKPHWTIGADVQYNFGKITTTSIEQVTGVQNGTSESNASTLSGANFDLGTMYQTKIYKKVNLFTSLSYTFSSNLNSENVREINVSGDPDPYAYPASTTKLKLPSRVIIGAGIGESRKWLVGTTLAFQGEGQLTNYYNAMDNVRYENYAKYAIGGYYIPNYTSFTSYLSRITYRAGLKYEKIGLIVNNESIKDVGMTLGAGIPIPGYFSNVNIGIEFGKKGTVSSNLVQENYVNFSVGFSFNDKWFVKSKFN

Entity 5 polymer

描述 description	Bam M
分子量 formula_weight	43899.3 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	D

MNKFKYYFVLLLAGLAIVSCNKKDDDEEIVPLRDYQEQYNTDNANIEEYLNTYFITVTDAPGEQTDQDVTFTKITDPSTQPSIMSYLNSPTFPKLLKREVPMHGIVYQMYYLVLREGTGTSPMNTDGAFTSYRGEYLTRVAKTDTEAEHLSTTFFEQVLFPTKALDLYGTIIGWSEAFPQFKTGTATMKPDGSMKYENFGAGVLFIPSGLGYYGSGASAIPAYSPLIFSIKLYDLTRLDHDLDGVFDFEEDINGDGYVYDFRNTTEYPTPPANQYDDDTDKDGIADFLDSDDDGDGYSTLFEITKPTGTEFLGGLSKYYPYNPVSDNPATPNYDETEKYGIPRRPTGELTNPNLPESINNPRKFIEDDYLAAGRKRIHLDNTYPYKKN

Entity 6 polymer

描述 description	Bam P
分子量 formula_weight	28413.7 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

MKNKLGVFVVCLFCQIMLGQNGTRKSLHGQVTNKSLAIESGYVMNINAKSRTFIGPGGLFDILAQPKDTLLFTGIAFQSKKIVLTEKDCSQILFSVSLDLVSNELKEVLVRKDLKVKSLDSNTQKYVDMQFEDDRQSTAKNTVMYSDQTIKYGTDFVRIFKDVKKLLSKNNEKEEVISDIAFVEYSKANFKPDFYTKTLGLKPDEVDLFLMFCSNDPESKRHLNEDQKFELIDFLINKNAEFKKVNAAQ

Entity 7 branched

描述 description	alpha-D-glucopyranuronic acid-(1-2)-[alpha-D-mannopyranose-(1-4)]beta-D-galactopyranose
分子量 formula_weight	518.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 8 branched

描述 description	alpha-D-glucopyranuronic acid-(1-2)-beta-D-galactopyranose
分子量 formula_weight	356.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 9 non-polymer

描述 description	DIACYL GLYCEROL
分子量 formula_weight	625.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 10 non-polymer

描述 description	;(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{S},3~{S},4~{R},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{R},5~{S},6~{R})-6-[(1~{S})-2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid ;
分子量 formula_weight	2975.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 11 non-polymer

描述 description	PHOSPHATIDYLETHANOLAMINE
分子量 formula_weight	734.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 12 non-polymer

描述 description	alpha-D-mannopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 13 non-polymer

描述 description	PALMITIC ACID
分子量 formula_weight	256.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 14 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	7

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	16

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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	2.700 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	2.70 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	55796

fit	/app/data/saxs_computation/n2/9n2d/9n2d.fit
pddf	/app/data/pr_computation/n2/9n2d/9n2d.pr.out
profile	/app/data/saxs_computation/n2/9n2d/9n2d.dat

Cryo-EM structure of an extended F. johnsoniae BAM complex, composite map

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

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 branched

Entity 8 branched

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-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)