SAXSdb — 5mfx

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

Genome polyprotein

Zika virus (strain Mr 766)

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–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 1685–2125	Fragment：UNP residues 1685-2125	;RNA (5'-R(PAPGPAPCPU)-3') ; × 1 ACT* ACETATE ION × 1 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；20% (w/v) ethylene glycol, 10% (w/v) polyethylene glycol 8000, 0.1 M MES/Imidazole pH 6.5, 20mM sodium formate, 20mM ammonium acetate, 20mM tri-sodium citrate, 20mM sodium potassium L-tartrate.	Resolution 1.60 Å R-free 0.191

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 5MFX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5TFN CRYSTAL STRUCTURE OF THE ZIKA VIRUS NS2B-NS3 PROTEASE in super-open conformation Deposited 2016-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1420–1466（47 aa）	Mutation：S135A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.6 mM protein, in 100 mM NaCl, 1.0 mM TCEP, 20 mM Tris-Cl buffer (pH 8.0) was mixed with the well solution (25% PEG3330, 200 mM NaCl and 100 mM BisTris pH 6.5)	Resolution 3.00 Å R-free 0.259
5TFN CRYSTAL STRUCTURE OF THE ZIKA VIRUS NS2B-NS3 PROTEASE in super-open conformation Deposited 2016-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1420–1466（47 aa）	Mutation：S135A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.6 mM protein, in 100 mM NaCl, 1.0 mM TCEP, 20 mM Tris-Cl buffer (pH 8.0) was mixed with the well solution (25% PEG3330, 200 mM NaCl and 100 mM BisTris pH 6.5)	Resolution 3.00 Å R-free 0.259
5TFN CRYSTAL STRUCTURE OF THE ZIKA VIRUS NS2B-NS3 PROTEASE in super-open conformation Deposited 2016-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1420–1466（47 aa） Chain B 1420–1466（47 aa）	Mutation：S135A Mutation：S135A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.6 mM protein, in 100 mM NaCl, 1.0 mM TCEP, 20 mM Tris-Cl buffer (pH 8.0) was mixed with the well solution (25% PEG3330, 200 mM NaCl and 100 mM BisTris pH 6.5)	Resolution 3.00 Å R-free 0.259
6RWZ Structure of Zika virus NS3 helicase in complex with ADP-BeF3 Deposited 2019-06-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1685–2125（441 aa）	Not recorded	MN MANGANESE (II) ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；20% w/v glycerol, 10% w/v polyethylene glycol 4000, 0.1 M MES/imidazole pH 6.5, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium citrate, and 20 mM sodium potassium L-tartrate.	Resolution 1.70 Å R-free 0.206
6S0J Structure of Zika virus NS3 helicase in complex with ADP-MgF3(H2O)- Deposited 2019-06-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1685–2125（441 aa）	Not recorded	KQB trifluoromagnesate monohydrate × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；15% PEG3350, 0.16 M sodium citrate and 9% ethylene glycol	Resolution 1.50 Å R-free 0.189

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A160JCU6_ZIKV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–451； UniProt 1685–2125

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	5mfx
Deposition date deposition_date	2016-11-18
Structure title title	Zika NS3 helicase:RNA complex
Keywords keywords	Helicase, RNA, hydrolase; HYDROLASE
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	23.23 Å
Radius of gyration Rg (electron density) rg_electron	22.41 Å
Forward intensity I(0) i0	43653100.00
Molecular weight molecular_weight	49036.0 kDa
Excluded volume excluded_volume	60482 Å³
Envelope volume envelope_volume	72512 Å³
Hydration-shell volume shell_volume	26635 Å³
Envelope diameter envelope_diameter	73.5 Å
Shell Rg shell_rg	29.78 Å
Envelope Rg envelope_rg	22.63 Å
Shape Rg shape_rg	22.43 Å
Total Rg total_rg	23.19 Å
Total atoms total_atoms	3442
Residues n_residues	439
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	71.1 Å
Rg (real space) rg_real	23.13 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	4.3650e+07
I(0) uncertainty (real space) i0_real_error	5.4320e+05
Rg (reciprocal space) rg_reciprocal	23.16 Å
I(0) (reciprocal space) i0_reciprocal	43650000.0000
Solution quality estimate total_estimate	0.9076
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.221
Kurtosis Kurtosis kurtosis	-0.491
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15090000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.962

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	50742.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3853

MGSSHHHHHHMLKKKQLTVLDLHPGAGKTRRVLPEIVREAIKTRLRTVILAPTRVVAAEMEEALRGLPVRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLYIMDEAHFTDPSSIAARGYISTRVEMGEAAAIFMTATPPGTRDAFPDSNSPIMDTEVEVPERAWSSGFDWVTDYSGKTVWFVPSVRNGNEIAACLTKAGKRVIQLSRKTFETEFQKTKHQEWDFVVTTDISEMGANFKADRVIDSRRCLKPVILDGERVILAGPMPVTHASAAQRRGRIGRNPNKPGDEYLYGGGCAETDEDHAHWLEARMLLDNIYLQDGLIASLYRPEADKVAAIEGEFKLRTEQRKTFVELMKRGDLPVWLAYQVASAGITYTDRRWCFDGTTNNTIMEDSVPAEVWTRHGEKRVLKPRWMDARVCSDHAALKSFKEFAAGKRGAAFGV

来源 Source

来源生物 organism	Zika virus (strain Mr 766)
通用名 common_name	ZIKV
NCBI Class编号 ncbi_taxonomy_id	64320
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(PAPGPAPCP*U)-3') ;
Molecular weight formula_weight	2815.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

AGACUCCAU

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	387

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5mfxA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5mfxA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	52.355 Å
Unit-cell length b length_b	73.037 Å
Unit-cell length c length_c	58.696 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.598 Å
Low-resolution limit resolution_low	45.690 Å
R factor r_factor	0.1634
R_work r_work	0.1619
R_free r_free	0.1914

fit	/app/data/saxs_computation/mf/5mfx/5mfx.fit
pddf	/app/data/pr_computation/mf/5mfx/5mfx.pr.out
profile	/app/data/saxs_computation/mf/5mfx/5mfx.dat

Zika NS3 helicase:RNA complex

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

Genome polyprotein

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)