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9va5

isochorismate synthase MenF with product salicylic acid and pyruvate

Method: X-RAY DIFFRACTION D_max: 66.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9va5
deposition_date	2025-06-02
last_revision	2026-06-10
title	isochorismate synthase MenF with product salicylic acid and pyruvate
keywords	Isochorismate synthase, MsMenF, Mycolicibacterium smegmatis, Crystal structure., BIOSYNTHETIC PROTEIN; BIOSYNTHETIC 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	21.23 Å
rg_electron	19.87 Å
i0	26076200.00
molecular_weight	38083.0 kDa
excluded_volume	47393 Å³
envelope_volume	55456 Å³
shell_volume	22881 Å³
envelope_diameter	69.7 Å
shell_rg	26.74 Å
envelope_rg	20.12 Å
shape_rg	19.86 Å
total_rg	20.82 Å
total_atoms	2683
n_residues	366
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	66.8 Å
rg_real	21.07 Å
rg_real_error	0.35 Å
i0_real	2.6080e+07
i0_real_error	3.2140e+05
rg_reciprocal	21.10 Å
i0_reciprocal	26080000.0000
total_estimate	0.8968
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.5 Å
skewness	0.099
kurtosis	-0.485
angular_range	— – 0.3750 Å⁻¹
current_alpha	0.0000
highest_alpha	6398000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.994

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	isochorismate synthase
formula_weight	37927.8 kDa
ec_number	5.4.4.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2930

PGSMSAPSFVFAGPSGVLIGEGVQTGFATIAGARAALTSGAADLVVGALPFDLTGPAALHAPASARVAGALPDWPTGTPPVLRTRETLPSGDVHRERVAEAVRRLRDADTPLDKVVLARALRLTAEAPWDPRTVLRRLADADPAATVYLADLSPAGDPHTGTVLVGASPELLVARDGDEVICRPFAGSAPRSADLETDRANAAALAASGKNRHEHELVVDVMRKALDPLCVDLQIAAQPELHATDALWHLSTPIRGRLRDKAITAIDLAVALHPTPAVGGVPTDLAASLITELEGDRGFYAGAVGWCDSAGNGRWVVSIRCAVLSADRRVALANAGGGIVAESDPDDEVDETTTKFRTILTGLGVQ

Source

organism	Mycolicibacterium smegmatis MC2 155
common_name	Mycobacterium smegmatis
ncbi_taxonomy_id	246196
host_organism	Escherichia coli

Entity 2 non-polymer

description	PYRUVIC ACID
formula_weight	88.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	2-HYDROXYBENZOIC ACID
formula_weight	138.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	247

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6. Citations (1)

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length_a	49.529 Å
length_b	60.931 Å
length_c	121.386 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.950 Å
resolution_low	30.470 Å
r_factor	0.2096
r_work	0.2063
r_free	0.2490

fit	/app/data/saxs_computation/va/9va5/9va5.fit
pddf	/app/data/pr_computation/va/9va5/9va5.pr.out
profile	/app/data/saxs_computation/va/9va5/9va5.dat

isochorismate synthase MenF with product salicylic acid and pyruvate

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