SAXSdb — 9up2

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1. Structure Basics

entry_id	9up2
deposition_date	2025-04-27
title	PvdL-E2-C3-A3-PCP3 in complex with MLP (NRPS cross-module)
keywords	Nonribosomal peptide synthetase, LIGASE, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	47.85 Å
rg_electron	48.28 Å
i0	489627000.00
molecular_weight	180220.0 kDa
excluded_volume	224830 Å³
envelope_volume	322070 Å³
shell_volume	60533 Å³
envelope_diameter	178.3 Å
shell_rg	46.90 Å
envelope_rg	47.61 Å
shape_rg	48.28 Å
total_rg	48.20 Å
total_atoms	25216
n_residues	1596
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	168.0 Å
rg_real	48.47 Å
rg_real_error	1.83 Å
i0_real	4.8960e+08
i0_real_error	1.0180e+07
rg_reciprocal	47.86 Å
i0_reciprocal	489200000.0000
total_estimate	0.7998
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	40.7 Å
skewness	0.574
kurtosis	-0.280
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	107900000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.708; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.810; Smooth: 0.457

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	PvdL
formula_weight	172528.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	25216

DSALTPIQHWFFDLPLARREHWNQALLLQPRQAIDLGLLRKSLQRLVEQHDALRLAFRQVDGEWLAQHRPLREQELLWHVPVQSFDECAELFAKAQRSLDLEQGPLLRAVLVDGPAGEQRLLLAIHHLVVDGVSWRVLLEDLQQVYRQFAEGAEPALPAKTSAFRDWAGRLQAYAGSESLREELGWWQARLGGQPVEWPCDRPQGDNREALAESVSLRLDPQRTRQLLQQAPAAYRTQVNDLLLTALARVLCRWSGQPSTLVQLEGHGREALFDDIDLTRSVGWFTSAYPLRLTPAQSPGESIKAIKEQLRAVPHKGLGYGVLRYLADPAVRQAMAALPTAPITFNYLGQFDQSFADALFQPLDQPTGPIHDEQAPLPNELSVDGQVYGGELVLRWTYSRERYDARTVNELAQAYLAELQALIEHCLEDGAGGLTPSDFPLAQLSQAQLDALAVPAGEIEDVYPLTPMQEGLLLHTLLEPGTGIYYMQDRYRIDSPLDPERFAAAWQAVVARHEALRASFVWNAGETMLQVIHKPGRTRIEFLDWSELPEDGHEERLQALHKREREAGFDLLEQPPFHLRLIRLGEARYWFMMSNHHILIDAWCRGLLMNDFFEIYSALGESRPANLPTPPRYRDYIAWLQRQDLEQSRRWWSESLRGFERPTLVPSDRPFLREHAGESGGMIVGDRYTRLDAADGARLRELAQRYQLTVNTFAQAAWALTLRRFSGERDVLFGVTVAGRPVGMPEMQRTVGLFINSIPLRVQMPAAGQRCTVREWLNRLFERNLELREHEHLPLVAIQESSELPKGQPLFDSLFVFENAPVEVSVLDRAQSLNASSDSGRTHTNFPLTVVCYPGDDLGLHLSYDQRYFEAPTVERLLGEFKRLLLALADGFHGELEALPLLGEDERDFLLDGCNRSARDYPLEQGYVRLFEAQVAAHPQRIAASCLEQRWSYAELNRRANRLGHALRAAGVGIDQPVALLAERGLDLLGMIVGSFKAGAGYLPLDPGHPTQRLTRIVELSRTLVLVCTQACREQALALFDELGCVDRPRLLVWDEIQQGEGAEHDPQVYSGPQNLAYVIYTSGSTGLPKGVMVEQAGMLNNQLSKVPYLELDENDVIAQTASQSFDISVWQFLAAPLFGARVAIVPNAVAHDPQGLLAHVGEQGITVLESVPSLIQGMLAEERQALDGLRWMLPTGEAMPPELARQWLKRYPRIGLVNAYGPAECSDDVAFFRVDLASTESTYLPIGSPTDNNRLYLLGAGADDAFELVPLGAVGELCVAGTGVGRGYVGDPLRTAQAFVPHPFGAPGERLYRTGDLARRRADGVLEYVGRIDHQVKIRGFRIELGEIEARLHERADVREAAVAVQEGANGKYLVGYLVPGETPRSSADSPAGLMVEQGAWFERIKQQLRADLPDYMVPLHWLVLDRMPLNANGKLDRKALPALDIGQMQNQAYQAPRNELEETLARIWAEVLKVERVGVFDNFFELGGHXLLATQIASRVQKALQRNVPLRAMFECTTVEELASYIESLAPSEI

Source

organism	Pseudomonas aeruginosa PAO1
ncbi_taxonomy_id	208964
host_organism	Escherichia coli

Entity 2 polymer

description	MbtH-like domain-containing protein
formula_weight	7288.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

DDIQFQVVVNHEEQYSIWPEYKEIPQGWRAAGKSGLKKDCLAYIEEVWTDMRPLSLRQHMD

Source

organism	Pseudomonas aeruginosa PAO1
ncbi_taxonomy_id	208964
host_organism	Escherichia coli

Entity 3 non-polymer

description	2,4-DIAMINOBUTYRIC ACID
formula_weight	118.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.33 Å
resolution_method	—
num_particles	165245

fit	/app/data/saxs_computation/up/9up2/9up2.fit
pddf	/app/data/pr_computation/up/9up2/9up2.pr.out
profile	/app/data/saxs_computation/up/9up2/9up2.dat

PvdL-E2-C3-A3-PCP3 in complex with MLP (NRPS cross-module)

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)