SAXSdb — 3vhs

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

ATPase WRNIP1

Homo sapiens

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 17–40 Chain B； UniProt 17–40	Fragment：UBIQUITIN-BINDING ZINC FINGER DOMAIN (UNP RESIDUES 17-40)	ZN ZINC ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；28% PEG 400, 0.1M HEPES, 0.2M calcium chrolide, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.90 Å R-free 0.262

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 3VHS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3VHT Crystal structure of GFP-Wrnip1 UBZ domain fusion protein in complex with ubiquitin Deposited 2011-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 9–46（38 aa） Fragment：GFP,Wrnip1 UBZ domain (UNP RESIDUES 9-46)	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2M DL-Malic acid, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 2.40 Å R-free 0.238

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

View Construct and Data Evidence

UniProt name	WRIP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–29； UniProt 17–40 Author chain B； PDBConstruct 6–29； UniProt 17–40

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	3vhs
Deposition date deposition_date	2011-09-06
Structure title title	Crystal structure of UBZ of human WRNIP1
Keywords keywords	ZINC FINGER, UBIQUITIN-BINDING DOMAIN, UBIQUITIN BINDING, METAL BINDING PROTEIN; METAL 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	12.05 Å
Radius of gyration Rg (electron density) rg_electron	11.49 Å
Forward intensity I(0) i0	1013610.00
Molecular weight molecular_weight	6046.0 kDa
Excluded volume excluded_volume	7283 Å³
Envelope volume envelope_volume	8368 Å³
Hydration-shell volume shell_volume	6860 Å³
Envelope diameter envelope_diameter	42.1 Å
Shell Rg shell_rg	15.89 Å
Envelope Rg envelope_rg	11.88 Å
Shape Rg shape_rg	11.57 Å
Total Rg total_rg	12.46 Å
Total atoms total_atoms	407
Residues n_residues	51
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	44.3 Å
Rg (real space) rg_real	12.09 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	1.0140e+06
I(0) uncertainty (real space) i0_real_error	1.2410e+04
Rg (reciprocal space) rg_reciprocal	12.09 Å
I(0) (reciprocal space) i0_reciprocal	1014000.0000
Solution quality estimate total_estimate	0.8342
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.0 Å
Skewness Skewness skewness	0.454
Kurtosis Kurtosis kurtosis	0.018
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	103700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.693; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.806; Smooth: 0.954

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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	ATPase WRNIP1
Molecular weight formula_weight	3243.8 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	423

GSPEFQVQCPVCQQMMPAAHINSHLDRCL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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8. Citations (1)

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Unit-cell length a length_a	36.482 Å
Unit-cell length b length_b	73.457 Å
Unit-cell length c length_c	34.651 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	23.770 Å
R factor r_factor	0.2153
R_work r_work	0.2128
R_free r_free	0.2615

fit	/app/data/saxs_computation/vh/3vhs/3vhs.fit
pddf	/app/data/pr_computation/vh/3vhs/3vhs.pr.out
profile	/app/data/saxs_computation/vh/3vhs/3vhs.dat

Crystal structure of UBZ of human WRNIP1

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

ATPase WRNIP1

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