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9q6g

PYCR2 complexed with NAD+ and (2S)-2-hydroxy-3,3-dimethylbutanoic acid

Method: X-RAY DIFFRACTION D_max: 116.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q6g
deposition_date	2025-08-22
title	PYCR2 complexed with NAD+ and (2S)-2-hydroxy-3,3-dimethylbutanoic acid
keywords	AMINO-ACID BIOSYNTHESIS, OXIDOREDUCTASE, PROLINE BIOSYNTHESIS; 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	36.45 Å
rg_electron	35.48 Å
i0	298830000.00
molecular_weight	129480.0 kDa
excluded_volume	157590 Å³
envelope_volume	218680 Å³
shell_volume	50920 Å³
envelope_diameter	120.7 Å
shell_rg	42.16 Å
envelope_rg	35.67 Å
shape_rg	35.57 Å
total_rg	35.66 Å
total_atoms	9070
n_residues	1336
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	116.5 Å
rg_real	36.34 Å
rg_real_error	1.08 Å
i0_real	2.9880e+08
i0_real_error	4.7400e+06
rg_reciprocal	36.41 Å
i0_reciprocal	298900000.0000
total_estimate	0.8949
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.8 Å
skewness	0.201
kurtosis	-0.458
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	105200000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.889

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Pyrroline-5-carboxylate reductase 2
formula_weight	33621.8 kDa
ec_number	1.5.1.2
mutation	K276Q
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E
atom_count	9079

MHHHHHHSSGVDLGTENLYFQSMSVGFIGAGQLAYALARGFTAAGILSAHKIIASSPEMNLPTVSALRKMGVNLTRSNKETVKHSDVLFLAVKPHIIPFILDEIGADVQARHIVVSCAAGVTISSVEKKLMAFQPAPKVIRCMTNTPVVVQEGATVYATGTHALVEDGQLLEQLMSSVGFCTEVEEDLIDAVTGLSGSGPAYAFMALDALADGGVKMGLPRRLAIQLGAQALLGAAKMLLDSEQHPCQLKDNVCSPGGATIHALHFLESGGFRSLLINAVEASCIRTRELQSMADQEQISPAALKKTLLDRVKLES

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	(2S)-2-hydroxy-3,3-dimethylbutanoic acid
formula_weight	132.2 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	9

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6. Citations (1)

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length_a	104.336 Å
length_b	109.936 Å
length_c	154.004 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	20

space_group	P 21 2 21
int_tables_number	18
crystal_system	—

resolution	2.650 Å
resolution_low	48.630 Å
r_factor	0.2686
r_work	0.2683
r_free	0.2843

fit	/app/data/saxs_computation/q6/9q6g/9q6g.fit
pddf	/app/data/pr_computation/q6/9q6g/9q6g.pr.out
profile	/app/data/saxs_computation/q6/9q6g/9q6g.dat