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9v7y

Crystal structure of class II HMG-CoA reductase from Ruegeria pomeroyi(Silicibacter pomeroyi))

Method: X-RAY DIFFRACTION D_max: 117.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v7y
deposition_date	2025-05-28
last_revision	2026-06-03
title	Crystal structure of class II HMG-CoA reductase from Ruegeria pomeroyi(Silicibacter pomeroyi))
keywords	HMG-CoA reductase, NAD, mevalonate pathway, OXIDOREDUCTASE; OXIDOREDUCTASE
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	39.91 Å
rg_electron	39.02 Å
i0	1042290000.00
molecular_weight	254780.0 kDa
excluded_volume	315130 Å³
envelope_volume	383540 Å³
shell_volume	77915 Å³
envelope_diameter	122.4 Å
shell_rg	47.75 Å
envelope_rg	38.41 Å
shape_rg	39.00 Å
total_rg	39.50 Å
total_atoms	17814
n_residues	2334
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	117.8 Å
rg_real	39.57 Å
rg_real_error	0.69 Å
i0_real	1.0420e+09
i0_real_error	1.8100e+07
rg_reciprocal	39.79 Å
i0_reciprocal	1043000000.0000
total_estimate	0.9047
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	53.0 Å
skewness	0.037
kurtosis	-0.657
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	308300000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.878

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	3-hydroxy-3-methylglutaryl coenzyme A reductase
formula_weight	44460.9 kDa
ec_number	1.1.1.88
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	17945

LNSRIEKMRDLDPAQRLVRVAEAAGLEPEAISALAGNGALPLSLANGMIENVIGKFELPLGVATNFTVNGRDYLIPMAVEEPSVVAAASYMARIARENGGFTAHGTAPLMRAQIQVVGLGDPEGARQRLLAHKAAFMEAADAVDPVLVGLGGGCRDIEVHVFRDTPVGAMVVLHLIVDVRDAMGANTVNTMAERLAPEVERIAGGTVRLRILSNLADLRLVRARVELAPETLTTQGYDGADVARGMVEACALAIVDPYRAATHNKGIMNGIDPVVVATGNDWRAIEAGAHAYAARTGHYTSLTRWELANDGRLVGTIELPLALGLVGGATKTHPTARAALALMQVETATELAQVTAAVGLAQNMAAIRALATEGIQRGHMTLHARNIAIMAGATGADIDRVTRVIVEAGDVSVARAKQVLENT

Source

organism	Ruegeria pomeroyi
ncbi_taxonomy_id	89184
host_organism	Escherichia coli

Entity 2 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	3-HYDROXY-3-METHYLGLUTARYL-COENZYME A
formula_weight	906.6 kDa
src_method	syn
entity_count	6

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	131

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6. Citations (1)

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length_a	71.686 Å
length_b	180.506 Å
length_c	203.890 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	24

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.640 Å
resolution_low	46.090 Å
r_factor	0.2003
r_work	0.1978
r_free	0.2487

fit	/app/data/saxs_computation/v7/9v7y/9v7y.fit
pddf	/app/data/pr_computation/v7/9v7y/9v7y.pr.out
profile	/app/data/saxs_computation/v7/9v7y/9v7y.dat

Crystal structure of class II HMG-CoA reductase from Ruegeria pomeroyi(Silicibacter pomeroyi))

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