SAXSdb — 9zgf

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1. Structure Basics

entry_id	9zgf
deposition_date	2025-12-02
title	The complex of HSV-1 proteins UL9 and ICP8 with forked DNA
keywords	DNA replication, protein-DNA complex, REPLICATION-DNA complex; REPLICATION/DNA
method	ELECTRON MICROSCOPY

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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	45.03 Å
rg_electron	44.15 Å
i0	815198000.00
molecular_weight	220400.0 kDa
excluded_volume	269670 Å³
envelope_volume	396830 Å³
shell_volume	74036 Å³
envelope_diameter	150.0 Å
shell_rg	49.95 Å
envelope_rg	43.12 Å
shape_rg	44.15 Å
total_rg	44.41 Å
total_atoms	15403
n_residues	1896
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	144.7 Å
rg_real	44.90 Å
rg_real_error	1.16 Å
i0_real	8.1520e+08
i0_real_error	1.2390e+07
rg_reciprocal	45.03 Å
i0_reciprocal	815300000.0000
total_estimate	0.8978
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	53.8 Å
skewness	0.185
kurtosis	-0.581
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	96530000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.859

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Major DNA-binding protein
formula_weight	128486.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	15403

METKPKTATTIKVPPGPLGYVYARACPSEGIELLALLSARSGDSDVAVAPLVVGLTVESGFEANVAVVVGSRTTGLGGTAVSLKLTPSHYSSSVYVFHGGRHLDPSTQAPNLTRLCERARRHFGFSDYTPRPGDLKHETTGEALCERLGLDPDRALLYLVVTEGFKEAVCINNTFLHLGGSDKVTIGGAEVHRIPVYPLQLFMPDFSRVIAEPFNANHRSIGEKFTYPLPFFNRPLNRLLFEAVVGPAAVALRCRNVDAVARAAAHLAFDENHEGAALPADITFTAFEASQGKTPRGGRDGGGKGAAGGFEQRLASVMAGDAALALESIVSMAVFDEPPTDISAWPLFEGQDTAAARANAVGAYLARAAGLVGAMVFSTNSALHLTEVDDAGPADPKDHSKPSFYRFFLVPGTHVAANPQVDREGHVVPGFEGRPTAPLVGGTQEFAGEHLAMLCGFSPALLAKMLFYLERCDGAVIVGRQEMDVFRYVADSNQTDVPCNLCTFDTRHACVHTTLMRLRARHPKFASAARGAIGVFGTMNSMYSDCDVLGNYAAFSALKRADGSETARTIMQETYRAATERVMAELETLQYVDQAVPTAMGRLETIITNREALHTVVNNVRQVVDREVEQLMRNLVEGRNFKFRDGLGEANHAMSLTLDPYACGPCPLLQLLGRRSNLAVYQDLALSQCHGVFAGQSVEGRNFRNQFQPVLRRRVMDMFNNGFLSAKTLTVALSEGAAICAPSLTAGQTAPAESSFEGDVARVTLGFPKELRVKSRVLFAGASANASEAAKARVASLQSAYQKPDKRVDILLGPLGFLLKQFHAAIFPNGKPPGSNQPNPQWFWTALQRNQLPARLLSREDIETIAFIKKFSLDYGAINFINLAPNNVSELAMYYMANQILRYCDHSTYFINTLTAIIAGSRRPPSVQAAAAWSAQGGAGLEAGARALMDAVDAHPGAWTSMFASCNLLRPVMAARPMVVLGLSISKYYGMAGNDRVFQAGNWASLMGGKNACPLLIFDRTRKFVLACPRAGFVCAASSLGGGAHESSLCEQLRGIISEGGAAVASSVFVATVKSLGPRTQQLQIEDWLALLEDEYLSEEMMELTARALERGNGEWSTDAALEVAHEAEALVSQLGNAGEVFNFGDFGCEDDNATPFGGPGAPGPAFAGRKRAFHGDDPFGEGPPDKKGDLTLDML

Source

organism	Human alphaherpesvirus 1 strain 17
ncbi_taxonomy_id	10299
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Replication origin-binding protein
formula_weight	94371.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MPFVGGAESGDPLGAGRPIGDDECEQYTSSVSLARMLYGGDLAEWVPRVHPKTTIERQQHGPVTFPNASAPTARCVTVVRAPMGSGKTTALIRWLREAIHSPDTSVLVVSCRRSFTQTLATRFAESGLVDFVTYFSSTNYIMNDRPFHRLIVQVESLHRVGPNLLNNYDVLVLDEVMSTLGQLYSPTMQQLGRVDALMLRLLRICPRIIAMDATANAQLVDFLCGLRGEKNVHVVVGEYAMPGFSARRCLFLPRLGTELLQAALRPPGPPSGPSPDASPEARGATFFGELEARLGGGDNICIFSSTVSFAEIVARFCRQFTDRVLLLHSLTPLGDVTTWGQYRVVIYTTVVTVGLSFDPLHFDGMFAYVKPMNYGPDMVSVYQSLGRVRTLRKGELLIYMDGSGARSEPVFTPMLLNHVVSSCGQWPAQFSQVTNLLCRRFKGRCDASACDTSLGRGSRIYNKFRYKHYFERCTLACLSDSLNILHMLLTLNCIRVRFWGHDDTLTPKDFCLFLRGVHFDALRAQRDLRELRCRDPEASLPAQAAETEEVGLFVEKYLRSDVAPAEIVALMRNLNSLMGRTRFIYLALLEACLRVPMATRSSAIFRRIYDHYATGVIPTINVTGELELVALPPTLNVTPVWELLCLCSTMAARLHWDSAAGGSGRTFGPDDVLDLLTPHYDRYMQLVFELGHCNVTDGLLLSEEAVKRVADALSGCPPRGSVSETDHAVALFKIIWGELFGVQMAKSTQTFPGAGRVKNLTKQTIVGLLDAHHIDHSACRTHRQLYALLMAHKREFAGARFKLRVPAWGRCLRTHSSSANPNADIILEAALSELPTEAWPMMQGAVNFSTL

Source

organism	Human alphaherpesvirus 1 strain 17
ncbi_taxonomy_id	10299
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	DNA (40-MER)
formula_weight	12184.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

CGAAGCGTTCGCACTTCGTCCCAATCTAACAATATCAATA

Entity 4 polymer

description	DNA (31-MER)
formula_weight	9579.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	E

ATACAATCAAGGACGAAGTGCGAACGCTTCG

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
formula_weight	523.2 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.100 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.10 Å
resolution_method	—
num_particles	411805

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

The complex of HSV-1 proteins UL9 and ICP8 with forked DNA

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

EM 3D

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)