9ilt

Crystal structure of alternative complex III from Chloroflexus aurantiacus

Method: X-RAY DIFFRACTION D_max: 154.3 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	9ilt
沉积日期 deposition_date	2024-07-01
最后修订 last_revision	2025-03-19
结构标题 title	Crystal structure of alternative complex III from Chloroflexus aurantiacus
关键词 keywords	;alternative complex III, Chloroflexus aurantiacus, photosynthetic electron transport chains, quinol: electron acceptor oxidoreductase, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
实验方法 method	X-RAY DIFFRACTION

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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	45.51 Å
回转半径 Rg (电子) rg_electron	45.32 Å
零角强度 I(0) i0	1042700000.00
分子量 molecular_weight	279400.0 kDa
排除体积 excluded_volume	353550 Å³
包络体积 envelope_volume	450790 Å³
水化壳体积 shell_volume	81170 Å³
包络直径 envelope_diameter	154.3 Å
壳层 Rg shell_rg	50.98 Å
包络 Rg envelope_rg	45.51 Å
形状 Rg shape_rg	45.35 Å
总 Rg total_rg	45.44 Å
总原子数 total_atoms	19668
残基数 n_residues	2461
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	154.3 Å
Rg (实空间) rg_real	45.55 Å
Rg 误差 (实空间) rg_real_error	1.08 Å
I(0) (实空间) i0_real	1.0430e+09
I(0) 误差 (实空间) i0_real_error	1.6020e+07
Rg (倒空间) rg_reciprocal	45.51 Å
I(0) (倒空间) i0_reciprocal	1043000000.0000
解质量估计 total_estimate	0.8797
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	48.5 Å
偏度 Skewness skewness	0.348
峰度 Kurtosis kurtosis	-0.462
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	244800000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.899

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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 (11)

Entity 1 polymer

描述 description	Cytochrome c7-like domain-containing protein
分子量 formula_weight	25247.0 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	A
原子数 atom_count	19668

MAQIFPRNANLLSRLSIFALVLLVVEGILILGVYFRSNYFRQVNVAIEQPVAFSHQLHVNVVGIDCRYCHTSVDQSYFANIPATETCMTCHSQIKTYSPLLEKVRESYATGKPIEWVKVYDLPNFVYFNHSIHVNKGIGCSTCHGQVNNMPVVWQQQALYMGWCLNCHRNPELYVRPREEVYNMDYVPPSNQLEIGRQLVAEYGIMPPDQLTNCYVCHR

Entity 2 polymer

描述 description	Fe-S-cluster-containing hydrogenase components 1-like protein
分子量 formula_weight	113115.4 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	B

MTQQQPDLEAIRAQLRDARGPQFWRSLDQLADAPAFRELIEREFPRGASELEDGISRRTFLKLMGASLALAGVTACTYQPRQYIAPFDRQPEGRVPGIPQYFASTLTLGGYGTGVLVRSNEGRPTKVEGNPRHPASLGGTDLFAQAEILTMYDPDRSTTVLRQGVPSTWAEFTTTLGNALTAARATQGAGVRLLTTTITSPSLAAQIEQFLQAYPQARWYQYEPINRDNVVAGARLAFGRDVTTRYDLSAAQVVVSLDADFLAPGPGFVAYARAFAERRKVRKDSTTMNRLYVVEASPSTTGTAADHRLPLRADAIAAFTGALANELGVGGAPATLSPKAEEFLRAIARDLEEHRGQSVVIAGDQQPPIVHALAHLINAELGNVGQTVFYHEPVEARPTNQTEELVALVSEMAAGRVETLIMIGGNPVYNAPGDLRFADRMASVPLTIHLSQFVDETSARATWHIPQAHPLESWGDARAFDGTASIVQPLIEPLYGGKTANELLAAMLGQPEAESYDLVRSFWLEQIGETGWQVALANGVIAETVAPVIEPTLNEGAIRATPIPQPGDGVEIVFRPDPSLFDGFYANNGWLQELPRPLTKLVWDNAALMSPRTAIKLLGLPFNADRLIGTEADDRERQQYLEQLSKVNGTIARIEYRGGIIEIPIWLLPGHAEDSITLNLGYGRTHAGRVGNNVGIDVYPIRTSDSPWFGAGARVTNTGRTYLLVSTQDHWTLEGRDIYRVGEFKKFKEDPKYIAKEVYQEEYGRETPNYQSLQPGDDYTGRNAWGMTINLNACIGCNACVVACQAENNIAVVGKDQVSRGREMHWIRIDRYFAGEDLDNPSIYMMPVNCMQCEKAPCEVVCPVAATVHDYEGLNNMVYNRCVGTKYCSNNCPYKVRRFNFLQYSDTTTETFKLAFNPDVTVRIRGVMEKCTYCVQRISGARIAAKRAAVQAGQSSYVISDGAIQTACEQACPTGAIVFGDINDSNSRVAKWKAEGHNYGLLGFLNTVPRTTYLARVRNPSEELEKVEG

Entity 3 polymer

描述 description	Polysulphide reductase NrfD
分子量 formula_weight	55223.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

MAQAQPLRTRPQDDGEAYLLPGETYTSISAKIGDVPLTPPLKTPKGWLAGFSVAFFMLMIFFVSVTWLFIRGVGIWGINIPVGWGMDIINFVWWIGIGHAGTLISAILLLLNQGWRNSINRFAEAMTLFAVACAGLYPILHLGRPWLFYWLIPYPNTHGMWPQFRSALAWDVFAISTYATVSLVFWLVGLIPDFATLRDRAKNIWVKRLYGIAALGWRGSARHWHRYEMASILLAGLSTPLVVSVHSIISLDFAISQVPGWQVTVFPPYFVAGAVFAGFAMVLLLMIPVRTFYGFENYITLHHLDVMAKVMLTTGMIVVYGYFMEVFASLYSGNEFEEYLLYNRLFGPSSWAYWGLLFCNAVAIQPLWFKKVRQNIPALLIISLIVSVGMWLERYVIIVISLERDFLPSSWDIYIPTIWDWSLYIGTFGLFFTLLFLFIRVLPMINIFEMRLFLYQETEKAKQRAGHGAHGHGHEQSPAHGAATAD

Entity 4 polymer

描述 description	Quinol:cytochrome c oxidoreductase membrane protein
分子量 formula_weight	19648.6 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

MRNDVYGVMAEFPTPEALIEATRKAKAAGYTKMDAFSPFPIEEVIEEIAHGDTGVPRLVLLFGLIGAASGFILQYIGNLVDYPLNVGGRPLDITNWPAMIPITFESGILLASFAAAIGMIVLNGLPSPYHPVFNVPRFQYASQDAFFLCIEATDPLFDRSRTSQFLRSLNPMQVSEVAY

Entity 5 polymer

描述 description	Cytochrome c domain-containing protein
分子量 formula_weight	23017.0 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	E

MQKPRLTSRMIRFGWVGLLVLLLTACHQDMYDQQKYTTYEPSSFFADGRSSRPNVPGTTPFEVVKTDEFLYTGLIDGQEVDAMPFPVTKDLLLRGQLKYNIYCAVCHGEAGYGASMVAERGGIVPANFHQQRLREAPLSHFFVVITNGVYRGDPENGGYQSMYGYASRITPEDRWAIAAYIRALQLSQNATIDDVPPDQRAQLGN

Entity 6 polymer

描述 description	Quinol:cytochrome c oxidoreductase quinone-binding subunit 2
分子量 formula_weight	45721.7 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	F

MATTSISQTRIPQLGQVQMLGLAAAVIGIGVLAAGYFLSPTSFFESYIYGYYVAMTIPLGCLGFLMVQHLTGGAWGVTVRRMLEAGAATLPIMGLLFIPIALGYFDTYKALGLEHPLYEWANPEVVTPGGAEFDPIIAHKVPWLSPLWVTARIAIFFIIWSALALTLRAWSRQQDAGGDAKKLATRMRRLSGIGVALFVITVTFFSFDVAMSLDPHWFSTIYGAHYMANAGLMTLAFLALMMSRVRDAALFREYVSVKPIHDIGKLIFAFTVLWTYMSYGQLVIIWSGDVAEFTPWYVHRTQHGWVFVALALMLFAFALPFFVLLFRGTKRNLNTLATIAGWIVVMRFVDMAWIILPEFREHLWDIAITDVAAPIGLIGLVIALFAANVQQAPLLPLRDPNMEQLQNSGHH

Entity 7 polymer

描述 description	ActG
分子量 formula_weight	12485.6 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	G

MSYRPNYSASRYTAGRPAQPVRTARTMAEPSLSRLMIAGLMVFLVLSLVVLLAGRLPFTPQPAPVTGNTYRTYVNDARTLLNSYGYTMEGKVHIPIDRAMDLIVERGLPVRE

Entity 8 polymer

描述 description	subunit I
分子量 formula_weight	4322.1 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

MQPEWSGDPEVKPVFLAVTLTGMVAFLLMVWLFAFYW

Entity 9 non-polymer

描述 description	HEME C
分子量 formula_weight	618.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 10 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 11 non-polymer

描述 description	FE3-S4 CLUSTER
分子量 formula_weight	295.8 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	142.016 Å
晶胞边长 b length_b	153.063 Å
晶胞边长 c length_c	173.381 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	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	3.250 Å
最低分辨率 resolution_low	40.300 Å
R 因子 r_factor	0.2507
R_work r_work	0.2490
R_free r_free	0.2858

fit	/app/data/saxs_computation/il/9ilt/9ilt.fit
pddf	/app/data/pr_computation/il/9ilt/9ilt.pr.out
profile	/app/data/saxs_computation/il/9ilt/9ilt.dat

Crystal structure of alternative complex III from Chloroflexus aurantiacus

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

衍射实验 Diffraction

5. 实体与聚合体信息 (11)

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 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)