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9qwm

Crystal structure of catalytic domain of Rv1625c bound to inhibitory Darpin G11

Method: X-RAY DIFFRACTION D_max: 80.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qwm
deposition_date	2025-04-14
last_revision	2026-04-29
title	Crystal structure of catalytic domain of Rv1625c bound to inhibitory Darpin G11
keywords	Adenylyl cyclase, Darpin, Mycobacterium tuberculosis, SIGNALING PROTEIN; SIGNALING PROTEIN
method	X-RAY DIFFRACTION

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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	23.32 Å
rg_electron	22.26 Å
i0	28001100.00
molecular_weight	39720.0 kDa
excluded_volume	49435 Å³
envelope_volume	63691 Å³
shell_volume	24104 Å³
envelope_diameter	82.4 Å
shell_rg	28.79 Å
envelope_rg	23.07 Å
shape_rg	22.23 Å
total_rg	23.18 Å
total_atoms	2798
n_residues	362
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	80.8 Å
rg_real	23.30 Å
rg_real_error	0.60 Å
i0_real	2.8000e+07
i0_real_error	3.9850e+05
rg_reciprocal	23.31 Å
i0_reciprocal	28000000.0000
total_estimate	0.8691
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.3 Å
skewness	0.346
kurtosis	-0.198
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	7194000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.786; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.963

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Adenylate cyclase
formula_weight	28202.8 kDa
ec_number	4.6.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2891

MGHHHHHHHHHHSSGLEVLFQGPSGHMRDTARAEAVMEAEHDRSEALLANMLPASIAERLKEPERNIIADKYDEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERLKDDFVLRERGHINVKGKGVMRTWYLIGRKVAAD

Source

organism	Mycobacterium tuberculosis
ncbi_taxonomy_id	1773
host_organism	Escherichia coli

Entity 2 polymer

description	Darpin G11
formula_weight	20055.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MRGSHHHHHHHHGSDLGKKLLEAATWGQHDEVRILMANGADVNAEDEWGMTPLHLAADSGHLEIVEVLLKTGADVNAMDWFGYTPLHLAAQMGHLEIVEVLLKTGADVNAMDREGYTPLHLAADSGHLEIVEVLLKHGADVNAQDKFGKTPFDLAAWEGNEDIAEVLQKAAKLNDYKDDDDK

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	93

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6. Citations (1)

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length_a	65.518 Å
length_b	65.518 Å
length_c	437.403 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65 2 2
int_tables_number	179
crystal_system	hexagonal

resolution	2.700 Å
resolution_low	47.600 Å
r_factor	0.2253
r_work	0.2214
r_free	0.2600

fit	/app/data/saxs_computation/qw/9qwm/9qwm.fit
pddf	/app/data/pr_computation/qw/9qwm/9qwm.pr.out
profile	/app/data/saxs_computation/qw/9qwm/9qwm.dat

Crystal structure of catalytic domain of Rv1625c bound to inhibitory Darpin G11

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

Refinement

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)