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9t2f

Crystal structure of human PRKCBP1 Zinc finger MYND-type containing 8 with pentaglutamate tag

Method: X-RAY DIFFRACTION D_max: 79.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t2f
deposition_date	2025-10-22
last_revision	2025-12-17
title	Crystal structure of human PRKCBP1 Zinc finger MYND-type containing 8 with pentaglutamate tag
keywords	Substrate Complex, Transcription, GDP-L-Fucose, L-Fucose; TRANSCRIPTION
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	24.65 Å
rg_electron	24.06 Å
i0	22562600.00
molecular_weight	35951.0 kDa
excluded_volume	44854 Å³
envelope_volume	59344 Å³
shell_volume	21315 Å³
envelope_diameter	80.1 Å
shell_rg	30.29 Å
envelope_rg	24.03 Å
shape_rg	24.12 Å
total_rg	24.72 Å
total_atoms	2508
n_residues	313
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	79.9 Å
rg_real	24.74 Å
rg_real_error	0.65 Å
i0_real	2.2560e+07
i0_real_error	3.3690e+05
rg_reciprocal	24.72 Å
i0_reciprocal	22560000.0000
total_estimate	0.8837
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.8 Å
skewness	0.361
kurtosis	-0.586
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	4644000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.876; Smooth: 0.956

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	MYND-type zinc finger-containing chromatin reader ZMYND8
formula_weight	38582.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2778

SMQDGRNDFYCWVCHREGQVLCCELCPRVYHAKCLRLTSEPEGDWFCPECEKITVAECIETQSKAMTMLTIEQLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVVIKICEHEMNEIEVCPECYLAACQKRDNWFCEPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVENIRRKFGVFNYSPFRTPYTPNSQYQMLLDPTNPSAGTAKIDKQEKVKLNFDMTASCEEEEE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	258

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6. Citations (1)

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length_a	108.040 Å
length_b	72.090 Å
length_c	68.670 Å
angle_alpha	90.00 °
angle_beta	127.02 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.680 Å
resolution_low	54.830 Å
r_factor	0.2134
r_work	0.2123
r_free	0.2361

fit	/app/data/saxs_computation/t2/9t2f/9t2f.fit
pddf	/app/data/pr_computation/t2/9t2f/9t2f.pr.out
profile	/app/data/saxs_computation/t2/9t2f/9t2f.dat

Crystal structure of human PRKCBP1 Zinc finger MYND-type containing 8 with pentaglutamate tag

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