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1kvp

STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY

Method: ELECTRON MICROSCOPY Dmax: 126.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SPV4 CAPSID PROTEIN VP1

Enterobacteria phage phiX174

UniProt P03641

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 × 60 PDB declaration: 60-MERIC（60） Consistent with protein copy count Chain A； UniProt 1–426 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 9.2；50 mM Sodium tetraborate cryo-EM vitrification conditions：Cryogen ETHANE Resolution 27.00 Å
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–426 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 9.2；50 mM Sodium tetraborate cryo-EM vitrification conditions：Cryogen ETHANE Resolution 27.00 Å
3 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain A； UniProt 1–426 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 9.2；50 mM Sodium tetraborate cryo-EM vitrification conditions：Cryogen ETHANE Resolution 27.00 Å
4 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–426 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 9.2；50 mM Sodium tetraborate cryo-EM vitrification conditions：Cryogen ETHANE Resolution 27.00 Å
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–426 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 9.2；50 mM Sodium tetraborate cryo-EM vitrification conditions：Cryogen ETHANE Resolution 27.00 Å

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 1KVP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: complete icosahedral assembly
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 280 PDB declaration: 280-meric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: 420-MERIC
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 280 PDB declaration: 280-meric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 180 PDB declaration: 240-MERIC
Chain 1 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain 1 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 15 PDB declaration: eicosameric
Chain 1 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Heteromer；Protein × 18 PDB declaration: 24-meric
Chain 1 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain 1 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å

3 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VGF_BPPHX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–497； UniProt 1–426

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 1kvp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1kvp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1kvp
Deposition date deposition_date1997-12-12
Structure title titleSTRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY
Keywords keywordsBACTERIOPHAGE SPV4 COAT PROTEIN, CHIMERA, Icosahedral virus, Virus; VIRUS
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.61 Å
Radius of gyration Rg (electron density) rg_electron33.97 Å
Forward intensity I(0) i048882200.00
Molecular weight molecular_weight55776.0 kDa
Excluded volume excluded_volume68026 ų
Envelope volume envelope_volume62685 ų
Hydration-shell volume shell_volume18678 ų
Envelope diameter envelope_diameter132.6 Å
Shell Rg shell_rg32.47 Å
Envelope Rg envelope_rg34.17 Å
Shape Rg shape_rg34.64 Å
Total Rg total_rg33.87 Å
Total atoms total_atoms—
Residues n_residues—
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 dmax126.3 Å
Rg (real space) rg_real34.19 Å
Rg uncertainty (real space) rg_real_error1.41 Å
I(0) (real space) i0_real4.8880e+07
I(0) uncertainty (real space) i0_real_error9.2680e+05
Rg (reciprocal space) rg_reciprocal33.83 Å
I(0) (reciprocal space) i0_reciprocal48870000.0000
Solution quality estimate total_estimate0.7369
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.6 Å
Skewness Skewness skewness0.764
Kurtosis Kurtosis kurtosis0.065
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3622000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.453; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.236; Smooth: 0.981
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1kvpa_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.5 — ssDNA viruses
Family Family familyb.121.5.1 — Microviridae-like VP
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8. Citations (3)

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9. Files and Curves (10)