SAXSdb — 5mhk

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1. Protein Identity and Related Structures Protein Identity & Related Structures

RS1

Human herpesvirus 1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Homooligomer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain C； UniProt 258–487 Chain D； UniProt 258–487 Chain J； UniProt 283–286	Fragment：LIkely N-terminus of chain D, but chain connectivity is ambiguous	;DNA (5'-D(GPCPTPCPCPGPTPGPTPGPGPAPCPGPAPTPCPGPG)-3') ; × 1 ;DNA (5'-D(GPCPTPCPCPGPTPGPTPGPGPAPCPGPAPTPCPGPG)-3') ; × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.2M Ammonium sulfate, 0.1 Bis/Tris pH 5.5 & 25% w/v PEG3350 [SG1 B8 Molecular Dimensions]. Cryoprotected with 20% PEG 200	Resolution 2.28 Å R-free 0.243
2	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 258–487 Chain B； UniProt 258–487	Fragment：LIkely N-terminus of chain D, but chain connectivity is ambiguous	;DNA (5'-D(GPCPTPCPCPGPTPGPTPGPGPAPCPGPAPTPCPGPG)-3') ; × 1 ;DNA (5'-D(GPCPTPCPCPGPTPGPTPGPGPAPCPGPAPTPCPGPG)-3') ; × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.2M Ammonium sulfate, 0.1 Bis/Tris pH 5.5 & 25% w/v PEG3350 [SG1 B8 Molecular Dimensions]. Cryoprotected with 20% PEG 200	Resolution 2.28 Å R-free 0.243

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q09I77_HHV1
Isoform	—
PDB entities	3, 4
Chains and sequence ranges	Author chain A； PDBConstruct 2–231； UniProt 258–487 Author chain B； PDBConstruct 2–231； UniProt 258–487 Author chain C； PDBConstruct 2–231； UniProt 258–487 Author chain D； PDBConstruct 2–231； UniProt 258–487 Author chain J； PDBConstruct 1–4； UniProt 283–286

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5mhk
Deposition date deposition_date	2016-11-24
Structure title title	ICP4 DNA-binding domain in complex with 19mer DNA duplex from its own promoter
Keywords keywords	Transcription factor, Herpes virus, Intercalation, transcription; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	34.26 Å
Radius of gyration Rg (electron density) rg_electron	32.95 Å
Forward intensity I(0) i0	227614000.00
Molecular weight molecular_weight	104290.0 kDa
Excluded volume excluded_volume	123250 Å³
Envelope volume envelope_volume	165320 Å³
Hydration-shell volume shell_volume	41972 Å³
Envelope diameter envelope_diameter	116.4 Å
Shell Rg shell_rg	39.52 Å
Envelope Rg envelope_rg	33.01 Å
Shape Rg shape_rg	32.89 Å
Total Rg total_rg	33.56 Å
Total atoms total_atoms	7272
Residues n_residues	845
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	114.6 Å
Rg (real space) rg_real	34.35 Å
Rg uncertainty (real space) rg_real_error	1.19 Å
I(0) (real space) i0_real	2.2760e+08
I(0) uncertainty (real space) i0_real_error	3.4500e+06
Rg (reciprocal space) rg_reciprocal	34.30 Å
I(0) (reciprocal space) i0_reciprocal	227600000.0000
Solution quality estimate total_estimate	0.8765
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.9 Å
Skewness Skewness skewness	0.406
Kurtosis Kurtosis kurtosis	-0.459
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	28290000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.928

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(GPCPTPCPCPGPTPGPTPGPGPAPCPGPAPTPCPGP*G)-3') ;
Molecular weight formula_weight	5877.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G,E
Atom count atom_count	7513

GCTCCGTGTGGACGATCGG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPCPTPCPCPGPTPGPTPGPGPAPCPGPAPTPCPGP*G)-3') ;
Molecular weight formula_weight	5775.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H,F

CCGATCGTCCACACGGAGC

Entity 3 Entity 3 polymer

Description description	RS1
Molecular weight formula_weight	24398.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,D,B

GPAASAGRIERRRARAAVAGRDATGRFTAGQPRRVELDADATSGAFYARYRDGYVSGEPWPGAGPPPPGRVLYGGLGDSRPGLWGAPEAEEARRRFEASGAPAAVWAPELGDAAQQYALITRLLYTPDAEAMGWLQNPRVVPGDVALDQACFRISGAARNSSSFITGSVARAVPHLGYAMAAGRFGWGLAHAAAAVAMSRRYDRAQKGFLLTSLRRAYAPLLARENAALTG

来源 Source

来源生物 organism	Human herpesvirus 1
通用名 common_name	HHV-1
NCBI Class编号 ncbi_taxonomy_id	10298
宿主生物 host_organism	ESCHERICHIA COLI

Entity 4 Entity 4 polymer

Description description	ICP4 DNA BINDING DOMAIN
Molecular weight formula_weight	394.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

FTAG

来源 Source

来源生物 organism	Human herpesvirus 1
通用名 common_name	HHV-1
NCBI Class编号 ncbi_taxonomy_id	10298
宿主生物 host_organism	ESCHERICHIA COLI

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	236

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8. Citations (1)

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Unit-cell length a length_a	61.510 Å
Unit-cell length b length_b	100.730 Å
Unit-cell length c length_c	201.890 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.280 Å
Low-resolution limit resolution_low	71.300 Å
R factor r_factor	0.2131
R_work r_work	0.2115
R_free r_free	0.2429

fit	/app/data/saxs_computation/mh/5mhk/5mhk.fit
pddf	/app/data/pr_computation/mh/5mhk/5mhk.pr.out
profile	/app/data/saxs_computation/mh/5mhk/5mhk.dat

ICP4 DNA-binding domain in complex with 19mer DNA duplex from its own promoter

1. Protein Identity and Related Structures Protein Identity & Related Structures

RS1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)