SAXSdb — 2j98

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

REPLICASE POLYPROTEIN 1AB

HUMAN CORONAVIRUS 229E

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 3825–3933 Chain B； UniProt 3825–3933	Fragment：RESIDUES 3825-3933 Mutation：YES	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；0.1M NA ACETATE PH 4.6 30% PEG MME 2000	Resolution 1.80 Å R-free 0.278

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 2J98	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2J97 Human coronavirus 229E non structural protein 9 (Nsp9) Deposited 2006-11-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3825–3933（109 aa） Fragment：RESIDUES 3825-3933	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；1.9M AMMONIUM SULFATE 0.1M NA ACETATE PH 4.0 5% MPD	Resolution 1.75 Å R-free 0.225
2ZU2 complex structure of CoV 229E 3CL protease with EPDTC Deposited 2008-10-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2966–3267（302 aa） Chain B 2966–3267（302 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 DTZ zinc(II)hydrogensulfide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；18% PEG 6000, 10% DMSO, 14% MPD, 0.1M Tris-HCL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.222
3EWQ HCov-229E Nsp3 ADRP domain Deposited 2008-10-16	Different construct Different mutation/modification 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 1269–1436（168 aa） Fragment：ADRP domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；0.1M HEPES pH 7.5, 25% w/v PEG 3350, VAPOR DIFFUSION, temperature 291.0K	Resolution 2.10 Å R-free 0.282
3EWR complex of substrate ADP-ribose with HCoV-229E Nsp3 ADRP domain Deposited 2008-10-16	Different construct Different mutation/modification 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 1269–1436（168 aa） Fragment：ADRP domain	Not recorded	APR ADENOSINE-5-DIPHOSPHORIBOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；0.1M HEPES pH 7.5, 25% w/v PEG 3350 , VAPOR DIFFUSION, temperature 291.0K	Resolution 2.01 Å R-free 0.264

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	R1A_CVH22
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–109； UniProt 3825–3933 Author chain B； PDBConstruct 1–109； UniProt 3825–3933

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	2j98
Deposition date deposition_date	2006-11-03
Structure title title	Human coronavirus 229E non structural protein 9 cys69ala mutant (Nsp9)
Keywords keywords	;SSB, HCOV, MEMBRANE, HELICASE, SARS COV, VIRAL REPLICASE, RNA REPLICATION, ATP-BINDING, NUCLEOTIDE-BINDING, RIBOSOMAL FRAMESHIFT, RNA-BINDING PROTEIN, RNA BINDING PROTEIN ;; RNA BINDING PROTEIN
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	19.85 Å
Radius of gyration Rg (electron density) rg_electron	18.85 Å
Forward intensity I(0) i0	9117170.00
Molecular weight molecular_weight	22930.0 kDa
Excluded volume excluded_volume	28998 Å³
Envelope volume envelope_volume	34089 Å³
Hydration-shell volume shell_volume	15864 Å³
Envelope diameter envelope_diameter	69.0 Å
Shell Rg shell_rg	24.04 Å
Envelope Rg envelope_rg	19.24 Å
Shape Rg shape_rg	18.83 Å
Total Rg total_rg	19.74 Å
Total atoms total_atoms	1613
Residues n_residues	208
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	69.8 Å
Rg (real space) rg_real	19.89 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	9.1170e+06
I(0) uncertainty (real space) i0_real_error	1.2700e+05
Rg (reciprocal space) rg_reciprocal	19.89 Å
I(0) (reciprocal space) i0_reciprocal	9117000.0000
Solution quality estimate total_estimate	0.7808
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.392
Kurtosis Kurtosis kurtosis	-0.314
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1489000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.758; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.872; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	REPLICASE POLYPROTEIN 1AB
Molecular weight formula_weight	12028.8 kDa
Mutation mutation	YES
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	1687

NNEIMPGKMKVKATKGEGDGGITSEGNALYNNEGGRAFMYAYVTTKPGMKYVKWEHDSGVVTVELEPPARFVIDTPTGPQIKYLYFVKNLNNLRRGAVLGYIGATVRLQ

来源 Source

来源生物 organism	HUMAN CORONAVIRUS 229E
通用名 common_name	HCOV 229E
NCBI Class编号 ncbi_taxonomy_id	11137
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	REPLICASE POLYPROTEIN 1AB
Molecular weight formula_weight	12026.8 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

NNEIKPGKMKVKATKGEGDGGITSEGNALYNNEGGRAFMYAYVTTKPGMKYVKWEHDSGVVTVELEPPARFVIDTPTGPQIKYLYFVKNLNNLRRGAVLGYIGATVRLQ

来源 Source

来源生物 organism	HUMAN CORONAVIRUS 229E
通用名 common_name	HCOV 229E
NCBI Class编号 ncbi_taxonomy_id	11137
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	2,3-DIHYDROXY-1,4-DITHIOBUTANE
Molecular weight formula_weight	154.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	74

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2j98a_
Class class	b — All beta proteins
Fold Fold fold	b.140 — Replicase NSP9
Superfamily Superfamily superfamily	b.140.1 — Replicase NSP9
Family Family family	b.140.1.0 — automated matches

Domain ID domain_id	d2j98b_
Class class	b — All beta proteins
Fold Fold fold	b.140 — Replicase NSP9
Superfamily Superfamily superfamily	b.140.1 — Replicase NSP9
Family Family family	b.140.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2j98A01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	250 — Replicase NSP9

Domain ID domain_id	2j98B01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	250 — Replicase NSP9

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8. Citations (1)

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Unit-cell length a length_a	26.396 Å
Unit-cell length b length_b	61.377 Å
Unit-cell length c length_c	107.309 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	4

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	53.680 Å
R factor r_factor	0.2180
R_work r_work	0.2140
R_free r_free	0.2780

fit	/app/data/saxs_computation/j9/2j98/2j98.fit
pddf	/app/data/pr_computation/j9/2j98/2j98.pr.out
profile	/app/data/saxs_computation/j9/2j98/2j98.dat

Human coronavirus 229E non structural protein 9 cys69ala mutant (Nsp9)

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

REPLICASE POLYPROTEIN 1AB

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)