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- PDB-1a92: OLIGOMERIZATION DOMAIN OF HEPATITIS DELTA ANTIGEN -

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Basic information

Entry
Database: PDB / ID: 1a92
TitleOLIGOMERIZATION DOMAIN OF HEPATITIS DELTA ANTIGEN
ComponentsDELTA ANTIGEN
KeywordsLEUCINE ZIPPER / COILED-COIL / OLIGOMERIZATION / HEPATITIS DELTA / HDV
Function / homology
Function and homology information


virion component / viral penetration into host nucleus / host cell / symbiont entry into host cell / host cell nucleus / RNA binding
Similarity search - Function
Delta antigen, N-terminal / Hepatitis delta virus delta antigen / Delta antigen, N-terminal / Hepatitis delta virus delta antigen / Light-harvesting Protein / Hepatitis delta antigen (HDAg) domain / Hepatitis delta antigen (HDAg) domain profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesHepatitis delta virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsZuccola, H.J. / Hogle, J.M.
Citation
Journal: Structure / Year: 1998
Title: Structural basis of the oligomerization of hepatitis delta antigen.
Authors: Zuccola, H.J. / Rozzelle, J.E. / Lemon, S.M. / Erickson, B.W. / Hogle, J.M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Self-Association of a Synthetic Peptide from the N Terminus of the Hepatitis Delta Virus Protein Into an Immunoreactive Alpha-Helical Multimer
Authors: Rozzelle Junior, J.E. / Wang, J.G. / Wagner, D.S. / Erickson, B.W. / Lemon, S.M.
History
DepositionApr 15, 1998Processing site: BNL
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DELTA ANTIGEN
B: DELTA ANTIGEN
C: DELTA ANTIGEN
D: DELTA ANTIGEN


Theoretical massNumber of molelcules
Total (without water)24,0244
Polymers24,0244
Non-polymers00
Water2,054114
1
A: DELTA ANTIGEN
C: DELTA ANTIGEN

A: DELTA ANTIGEN
C: DELTA ANTIGEN

B: DELTA ANTIGEN
D: DELTA ANTIGEN

B: DELTA ANTIGEN
D: DELTA ANTIGEN


Theoretical massNumber of molelcules
Total (without water)48,0488
Polymers48,0488
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_645-x+3/2,y-1/2,-z1
crystal symmetry operation4_565x+1/2,-y+3/2,-z1
Buried area16830 Å2
ΔGint-151 kcal/mol
Surface area23070 Å2
MethodPISA
2
A: DELTA ANTIGEN
C: DELTA ANTIGEN


Theoretical massNumber of molelcules
Total (without water)12,0122
Polymers12,0122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-26 kcal/mol
Surface area7570 Å2
MethodPISA
3
B: DELTA ANTIGEN
D: DELTA ANTIGEN


Theoretical massNumber of molelcules
Total (without water)12,0122
Polymers12,0122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-25 kcal/mol
Surface area7480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.220, 85.300, 29.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-84-

HOH

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Components

#1: Protein/peptide
DELTA ANTIGEN / HEPATITIS DELTA ANTIGEN


Mass: 6006.051 Da / Num. of mol.: 4 / Fragment: OLIGOMERIZATION DOMAIN / Mutation: INS (K60-Y)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis delta virus / Genus: Deltavirus / References: UniProt: P25989
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.78 %
Crystal growpH: 5.2 / Details: pH 5.2
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlpeptide1drop
2100 mMsodium acetate1drop
3100 mMsodium citrate1drop
4100 mMsodium acetate1reservoir
5100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jun 1, 1996 / Details: MIRRORS
RadiationMonochromator: CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 28279 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.038 / Net I/σ(I): 51
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 7 / Rsym value: 0.2 / % possible all: 94
Reflection
*PLUS
Num. measured all: 221286
Reflection shell
*PLUS
% possible obs: 35 % / Rmerge(I) obs: 0.18

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2600 10.1 %RANDOM
Rwork0.227 ---
obs0.227 25735 97.8 %-
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 0 114 1784
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d16.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.59
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it7.841.5
X-RAY DIFFRACTIONx_mcangle_it7.752
X-RAY DIFFRACTIONx_scbond_it17.232
X-RAY DIFFRACTIONx_scangle_it20.622.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 418 10.2 %
Rwork0.344 3697 -
obs--95.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.225 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg16.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.59

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