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9vgw

Crystal structure of human PCNA in complex with REV1 PIP-box

Method: X-RAY DIFFRACTION D_max: 99.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vgw
deposition_date	2025-06-15
title	Crystal structure of human PCNA in complex with REV1 PIP-box
keywords	nuclear protein, DNA replication, DNA BINDING PROTEIN; DNA BINDING 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	33.36 Å
rg_electron	32.13 Å
i0	110803000.00
molecular_weight	84535.0 kDa
excluded_volume	106260 Å³
envelope_volume	143910 Å³
shell_volume	36124 Å³
envelope_diameter	100.1 Å
shell_rg	40.80 Å
envelope_rg	30.97 Å
shape_rg	32.12 Å
total_rg	32.93 Å
total_atoms	5910
n_residues	767
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	99.8 Å
rg_real	33.21 Å
rg_real_error	0.72 Å
i0_real	1.1080e+08
i0_real_error	1.7370e+06
rg_reciprocal	33.31 Å
i0_reciprocal	110800000.0000
total_estimate	0.9046
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	3
r_peak_primary	48.8 Å
skewness	-0.013
kurtosis	-0.838
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	57430000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.954

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Proliferating cell nuclear antigen
formula_weight	28795.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	5940

MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEGS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	peptide from DNA repair protein REV1
formula_weight	1514.7 kDa
ec_number	2.7.7.-
src_method	syn
entity_count	3

Polymer

type	polypeptide(L)
strand_id	X,Y,Z

SPQKLIDGFLKHE

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	30

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6. Citations (1)

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length_a	145.221 Å
length_b	72.508 Å
length_c	83.599 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	2.700 Å
resolution_low	43.770 Å
r_factor	0.2165
r_work	0.2141
r_free	0.2606

fit	/app/data/saxs_computation/vg/9vgw/9vgw.fit
pddf	/app/data/pr_computation/vg/9vgw/9vgw.pr.out
profile	/app/data/saxs_computation/vg/9vgw/9vgw.dat

Crystal structure of human PCNA in complex with REV1 PIP-box

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

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)