SAXSdb — 9be4

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9be4
沉积日期 deposition_date	2024-04-13
结构标题 title	The post-condensation state of the dimodular NRPS protein LgrA
关键词 keywords	Nornribosomal peptide synthetase, Condensation, Peptide bond, Linear gramicidin, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	62.12 Å
回转半径 Rg (电子) rg_electron	61.91 Å
零角强度 I(0) i0	4249390000.00
分子量 molecular_weight	366540.0 kDa
排除体积 excluded_volume	355580 Å³
包络体积 envelope_volume	760880 Å³
水化壳体积 shell_volume	99386 Å³
包络直径 envelope_diameter	256.5 Å
壳层 Rg shell_rg	69.10 Å
包络 Rg envelope_rg	59.65 Å
形状 Rg shape_rg	61.92 Å
总 Rg total_rg	61.97 Å
总原子数 total_atoms	27803
残基数 n_residues	3518
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	215.6 Å
Rg (实空间) rg_real	62.06 Å
Rg 误差 (实空间) rg_real_error	2.18 Å
I(0) (实空间) i0_real	4.2490e+09
I(0) 误差 (实空间) i0_real_error	8.7520e+07
Rg (倒空间) rg_reciprocal	62.12 Å
I(0) (倒空间) i0_reciprocal	4250000000.0000
解质量估计 total_estimate	0.8781
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	86.2 Å
偏度 Skewness skewness	0.211
峰度 Kurtosis kurtosis	-0.432
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	82600000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.862

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	Linear gramicidin synthase subunit A
分子量 formula_weight	206246.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	28158

MGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAFADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQLAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTSGSTGLAKGVMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNGYGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLDNLVKIRGYRIEPGEIEPFLMNHPLIELTTVLAKEQADGRKYLVGYYVAPEEIPHGELREWLGNDLPDYMIPTYFVHMKAFPLTANGKVDRRALPDVQADAELLGEDYVAPTDELEQQLAQVWSHVLGIPQMGIDDHFLERGGDXIKVMQLIHQLKNIGLSLRYDQLFTHPTIRQLKRLLTEQKQVNGLLEPLRELDEQAEYETSAVEKRMYIIQQQDVESIAYNVVYTINFPLTVDTEQIRVALEQLVLRHEGLRSTYHMRGDEIVKRIVPRAELSFVRQTGEEESVQSLLAEQIKPFDLAKAPLLRAGVIETADKKVLWFDSHHILLDGLSKSILARELQALLGQQVLSPVEKTYKSFARWQNEWFASDEYEQQIAYWKTLLQGELPAVQLPTKKRPPQLTFDGAIQMYRVNPEITRKLKATAAKHDLTLYMLMLTIVSIWLSKMNSDSNQVILGTVTDGRQHPDTRELLGMFVNTLPLLLSIDHEESFLHNLQQVKAKLLPALQNQYVPFDKILEAARVKREGNRHPLFDVMFMMQGAPETELESNMHHINAGISKFDLTLEVLERENGLNIVFEYNTHLFDEGMILRMVAQFEHLLLQAVHGLDQQVKRFELVTEDEKRDLFLRVNDTAKAYPNKLIMSMLEDWAAATPDKTALVFREQRVTYRELNERVNQLAHTLREKGVQPDDLVMLMAERSVEMMVAIFAVLKAGGAYLPIDPHSPAERIAYIFADSGAKLVLAQSPFVEKASMAEVVLDLNSASSYAADTSNPPLVNQPGDLVYVMYTSGSTGKPKGVMIEHGALLNVLHGMQDEYPLLQDDAFLLKTTYIFDISVAEIFGWVPGRGKLVILEPEAEKNPKAIWQAVVGAGITHINFVPSMLIPFVEYLEGRTEANRLRYILACGEAMPDELVPKVYEVLPEVKLENIYGPTEATIYASRYSLAKGSQESPVPIGKPLPNYRMYIINRHGQLQPIGVPGELCIAGASLARGYLNNPALTEEKFTPHPLEKGERIYRTGDLARYREDGNIEYLGRMDHQVKIRGYRIELDEIRSKLIQEETIQDAVVVARNDQNGQAYLCAYLLSEQEWTVGQLRELLRRELPEYMIPAHFVLLKQFPLTANGKLDRKALPEPDGSVKAEAEYAAPRTELEATLAHIWGEVLGIERIGIRDNFFELGGDSIKGLQIASRLQRINWTMVINHLFLYPTIEQIAPFVTSEQVVIEAAAENLYFQ

来源 Source

来源生物 organism	Brevibacillus parabrevis
NCBI 分类编号 ncbi_taxonomy_id	54914
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	;N-formyl-L-valyl-N-[2-({N-[(2S)-2-hydroxy-4-{[(S)-hydroxy(oxo)-lambda~5~-phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]glycinamide ;
分子量 formula_weight	525.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	350

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	184.406 Å
晶胞边长 b length_b	426.580 Å
晶胞边长 c length_c	77.298 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	8

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	orthorhombic

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	49.870 Å
R 因子 r_factor	0.2189
R_work r_work	0.2180
R_free r_free	0.2575

fit	/app/data/saxs_computation/be/9be4/9be4.fit
pddf	/app/data/pr_computation/be/9be4/9be4.pr.out
profile	/app/data/saxs_computation/be/9be4/9be4.dat

The post-condensation state of the dimodular NRPS protein LgrA

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