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9z6r

Crystal Structure of CBS domain containing protein from Burkholderia phymatum

Method: X-RAY DIFFRACTION D_max: 69.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z6r
deposition_date	2025-11-14
last_revision	2025-11-26
title	Crystal Structure of CBS domain containing protein from Burkholderia phymatum
keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, CBS domain containing protein, Burkholderia phymatum, UNKNOWN FUNCTION ;; UNKNOWN FUNCTION
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	21.06 Å
rg_electron	20.18 Å
i0	13171000.00
molecular_weight	25992.0 kDa
excluded_volume	32131 Å³
envelope_volume	39778 Å³
shell_volume	17194 Å³
envelope_diameter	69.7 Å
shell_rg	25.64 Å
envelope_rg	20.30 Å
shape_rg	20.22 Å
total_rg	20.86 Å
total_atoms	1808
n_residues	237
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	69.0 Å
rg_real	21.08 Å
rg_real_error	0.38 Å
i0_real	1.3170e+07
i0_real_error	1.6600e+05
rg_reciprocal	21.08 Å
i0_reciprocal	13170000.0000
total_estimate	0.7158
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	21.3 Å
skewness	0.335
kurtosis	-0.459
angular_range	— – 0.3750 Å⁻¹
current_alpha	0.0000
highest_alpha	4264000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 0.225; Positv: 1.000; Valcen: 0.952; Smooth: 0.994

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	CBS domain containing protein
formula_weight	14070.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2021

MAHHHHHHMTTVAEVMTRDLATIGPSQSLREAAKMMDDLNVGSLPVCDGVNLIGMLTDRDIVVRAVSAGVAPNERIEGVVSGPPDWCYEDDDVDTVRKKMEEAQIRRVPVVDREKRLVGILSLGDLAT

Source

organism	Paraburkholderia phymatum STM815
ncbi_taxonomy_id	391038
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	156

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6. Citations (1)

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length_a	41.947 Å
length_b	40.742 Å
length_c	67.579 Å
angle_alpha	90.00 °
angle_beta	93.11 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.390 Å
resolution_low	41.890 Å
r_factor	0.1641
r_work	0.1623
r_free	0.1937

fit	/app/data/saxs_computation/z6/9z6r/9z6r.fit
pddf	/app/data/pr_computation/z6/9z6r/9z6r.pr.out
profile	/app/data/saxs_computation/z6/9z6r/9z6r.dat