SAXSdb — 4blg

▼

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

LATENCY-ASSOCIATED NUCLEAR ANTIGEN

Murid herpesvirus 4

UniProt O41974

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 140–272 Chain B； UniProt 140–272	Fragment：DNA-BINDNG DOMAIN, RESIDUES 140-272	PO4 PHOSPHATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；0.1 M NA/K PHOSPHATE PH 7.0, 0.1 M LITHIUM SULPHATE, 22 % W/V PEG 3350 AND 4 % V/V 1,4 DIOXANE.	Resolution 2.20 Å R-free 0.203

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.

Other PDB	Difference from Current Entry 4BLG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2YQ1 MHV-68 LANA (ORF73) C-terminal domain: triclinic crystal form Deposited 2012-11-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 124–260（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 124-260 Chain D 124–260（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 124-260	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；1.5 UL OF 0.3 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 5 MM DTT WERE ADDED TO 1.5 UL OF 2.0 M SODIUM FORMATE, 15% (W/V) PEG 6000. THE MIXTURE WAS INCUBATED AT 20 DEGREE CENTIGRADE IN A HANGING DROP SETUP. CRYSTALS GREW IN A FEW DAYS AND WERE CRYO-PROTECTED BY SHORT SOAKING IN 2.0 M SODIUM FORMATE, 15% (W/V) PEG 6000, 25% (V/V) GLYCEROL.	Resolution 2.30 Å R-free 0.246
2YQ1 MHV-68 LANA (ORF73) C-terminal domain: triclinic crystal form Deposited 2012-11-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 124–260（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 124-260 Chain B 124–260（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 124-260	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；1.5 UL OF 0.3 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 5 MM DTT WERE ADDED TO 1.5 UL OF 2.0 M SODIUM FORMATE, 15% (W/V) PEG 6000. THE MIXTURE WAS INCUBATED AT 20 DEGREE CENTIGRADE IN A HANGING DROP SETUP. CRYSTALS GREW IN A FEW DAYS AND WERE CRYO-PROTECTED BY SHORT SOAKING IN 2.0 M SODIUM FORMATE, 15% (W/V) PEG 6000, 25% (V/V) GLYCEROL.	Resolution 2.30 Å R-free 0.246

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	O41974_MHV68
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–141； UniProt 140–272 Author chain B； PDBConstruct 9–141； UniProt 140–272

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4blg
Deposition date deposition_date	2013-05-02
Structure title title	Crystal structure of MHV-68 Latency-associated nuclear antigen (LANA) C-terminal DNA binding domain
Keywords keywords	VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	19.86 Å
Radius of gyration Rg (electron density) rg_electron	18.38 Å
Forward intensity I(0) i0	13937800.00
Molecular weight molecular_weight	28079.0 kDa
Excluded volume excluded_volume	35243 Å³
Envelope volume envelope_volume	40757 Å³
Hydration-shell volume shell_volume	18585 Å³
Envelope diameter envelope_diameter	64.6 Å
Shell Rg shell_rg	24.48 Å
Envelope Rg envelope_rg	18.67 Å
Shape Rg shape_rg	18.34 Å
Total Rg total_rg	19.40 Å
Total atoms total_atoms	1965
Residues n_residues	240
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

▼

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

Maximum dimension Dmax dmax	65.0 Å
Rg (real space) rg_real	19.78 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.3940e+07
I(0) uncertainty (real space) i0_real_error	1.6460e+05
Rg (reciprocal space) rg_reciprocal	19.80 Å
I(0) (reciprocal space) i0_reciprocal	13940000.0000
Solution quality estimate total_estimate	0.8915
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.242
Kurtosis Kurtosis kurtosis	-0.418
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3023000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.992

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	LATENCY-ASSOCIATED NUCLEAR ANTIGEN
Molecular weight formula_weight	15981.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2027

GPGYQKDPPKKYQGMRRHLQVTAPRLFDPEGHPPTHFKSAVMFSSTHPYTLNKLHKCIQSKHVLSTPVSCLPLVPGTTQQCVTYYLLSFVEDKKQAKKLKRVVLAYCEKYHSSVEGTIVKAKPYFPLPEPPTEPPTDPEQP

来源 Source

来源生物 organism	Murid herpesvirus 4
通用名 common_name	MURINE HERPESVIRUS 68
NCBI Class编号 ncbi_taxonomy_id	33708
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	62

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4blgA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

Domain ID domain_id	4blgB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	88.575 Å
Unit-cell length b length_b	61.680 Å
Unit-cell length c length_c	63.678 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.36 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	30.840 Å
R factor r_factor	0.1731
R_work r_work	0.1714
R_free r_free	0.2032

fit	/app/data/saxs_computation/bl/4blg/4blg.fit
pddf	/app/data/pr_computation/bl/4blg/4blg.pr.out
profile	/app/data/saxs_computation/bl/4blg/4blg.dat

Crystal structure of MHV-68 Latency-associated nuclear antigen (LANA) C-terminal DNA binding domain

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

LATENCY-ASSOCIATED NUCLEAR ANTIGEN

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