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9zg5

Structure of superfolder GFP bound to nanobody 15

Method: X-RAY DIFFRACTION D_max: 139.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zg5
deposition_date	2025-12-02
last_revision	2026-06-03
title	Structure of superfolder GFP bound to nanobody 15
keywords	GFP, nanobody, FLUORESCENT PROTEIN; FLUORESCENT 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	41.10 Å
rg_electron	40.79 Å
i0	407586000.00
molecular_weight	160990.0 kDa
excluded_volume	199900 Å³
envelope_volume	275550 Å³
shell_volume	57660 Å³
envelope_diameter	147.4 Å
shell_rg	45.22 Å
envelope_rg	39.74 Å
shape_rg	40.81 Å
total_rg	40.95 Å
total_atoms	11330
n_residues	1447
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	139.7 Å
rg_real	41.15 Å
rg_real_error	1.37 Å
i0_real	4.0760e+08
i0_real_error	7.4330e+06
rg_reciprocal	41.10 Å
i0_reciprocal	407600000.0000
total_estimate	0.8698
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	47.8 Å
skewness	0.412
kurtosis	-0.178
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	21510000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.803; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.895

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Green fluorescent protein
formula_weight	27025.3 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,E,G
atom_count	11330

GSLSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLXVQCFSRYPDHMKQHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHELEYNFNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHGMDELYKK

Source

organism	Aequorea victoria
ncbi_taxonomy_id	6100
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

description	Nanobody 15
formula_weight	13913.6 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	C,D,F,H

GSQVQLVESGGGAVQSGGSLSLSCAASGGIRSISAMTWFRQAPGREREFVAAVTRTLGTTYYTDSVKGRFTISRDSVKGTLYLRMNNMRPEDAAVYYCAARTRGFSTKVALETTDGMDYWGKGTLVTVSS

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli B

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

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6. Citations (1)

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length_a	169.050 Å
length_b	169.050 Å
length_c	70.790 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 32
int_tables_number	145
crystal_system	—

resolution	3.400 Å
resolution_low	34.400 Å
r_factor	0.2968
r_work	0.2950
r_free	0.3313

fit	/app/data/saxs_computation/zg/9zg5/9zg5.fit
pddf	/app/data/pr_computation/zg/9zg5/9zg5.pr.out
profile	/app/data/saxs_computation/zg/9zg5/9zg5.dat

Structure of superfolder GFP bound to nanobody 15

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

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)