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4p5i

Crystal structure of the chemokine binding protein from orf virus

Method: X-RAY DIFFRACTION Dmax: 73.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chemokine binding protein

Orf virus

UniProt Q2F862

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 17–286 Fragment：UNP RESIDUES 17-286 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；CRYSTALLIZATION DROPLETS CONSISTED OF 3 UL ORFV CKBP (12 MG ML-1 IN 20 MM HEPES PH 7.0, 1 MM DTT) PLUS 3.0 UL OF A SOLUTION CONTAINING 100 MM L-ARG IN 1.8 M AMMONIUM CITRATE TRIBASIC PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K Resolution 2.25 Å R-free 0.233

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 4P5I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4ZK9 The chemokine binding protein of orf virus complexed with CCL2 Deposited 2015-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 17–286（270 aa） Fragment：UNP residues 17-286
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dihydrate pH5.6, 2.0M ammonium citrate
Resolution 2.60 Å R-free 0.281
4ZKB The chemokine binding protein of orf virus complexed with CCL3 Deposited 2015-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 17–286（270 aa） Fragment：UNP residues 17-286
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dihydrate pH5.6, 2.0M ammonium citrate
Resolution 2.90 Å R-free 0.323
4ZKC The chemokine binding protein of orf virus complexed with CCL7 Deposited 2015-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 17–286（270 aa） Fragment：UNP residues 17-286
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dihydrate pH5.6, 2.0M ammonium citrate
Resolution 3.15 Å R-free 0.327

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

View Construct and Data Evidence
UniProt name Q2F862_ORFV
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–270； UniProt 17–286

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.

SAXS scattering curve SAXS Profile

SAXS profile for 4p5i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4p5i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4p5i
Deposition date deposition_date2014-03-17
Structure title titleCrystal structure of the chemokine binding protein from orf virus
Keywords keywordsHOST CHEMOKINES, SECRETED, CYTOKINE, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.73 Å
Radius of gyration Rg (electron density) rg_electron19.65 Å
Forward intensity I(0) i014118000.00
Molecular weight molecular_weight27006.0 kDa
Excluded volume excluded_volume33333 ų
Envelope volume envelope_volume42183 ų
Hydration-shell volume shell_volume18458 ų
Envelope diameter envelope_diameter75.7 Å
Shell Rg shell_rg25.59 Å
Envelope Rg envelope_rg20.50 Å
Shape Rg shape_rg19.67 Å
Total Rg total_rg20.46 Å
Total atoms total_atoms1894
Residues n_residues240
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax73.7 Å
Rg (real space) rg_real20.77 Å
Rg uncertainty (real space) rg_real_error0.63 Å
I(0) (real space) i0_real1.4120e+07
I(0) uncertainty (real space) i0_real_error1.8340e+05
Rg (reciprocal space) rg_reciprocal20.76 Å
I(0) (reciprocal space) i0_reciprocal14120000.0000
Solution quality estimate total_estimate0.7759
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.5 Å
Skewness Skewness skewness0.456
Kurtosis Kurtosis kurtosis-0.009
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2751000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.716; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; 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)

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8. Citations (1)

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9. Files and Curves (10)