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- PDB-4bmg: Crystal structure of hexameric HBc149 Y132A -

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Basic information

Entry
Database: PDB / ID: 4bmg
TitleCrystal structure of hexameric HBc149 Y132A
ComponentsCAPSID PROTEIN
KeywordsVIRAL PROTEIN / PROTEIN FOLDING / ALLOSTERY
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / identical protein binding
Similarity search - Function
Hepatitis B viral capsid (hbcag) fold / Viral capsid, core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHEPATITIS B VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJuergens, M.C. / Alexander, C.G. / Shepherd, D.A. / Ashcroft, A.E. / Ferguson, N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Thermodynamic Origins of Protein Folding, Allostery and Capsid Formation in the Human Hepatitis B Virus Core Protein
Authors: Alexander, C.G. / Juergens, M.C. / Shepherd, D.A. / Freund, S. / Ashcroft, A.E. / Ferguson, N.
History
DepositionMay 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAPSID PROTEIN
B: CAPSID PROTEIN
C: CAPSID PROTEIN
D: CAPSID PROTEIN
E: CAPSID PROTEIN
F: CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)104,1536
Polymers104,1536
Non-polymers00
Water00
1
C: CAPSID PROTEIN
D: CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,7182
Polymers34,7182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-36.9 kcal/mol
Surface area13960 Å2
MethodPISA
2
A: CAPSID PROTEIN
B: CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,7182
Polymers34,7182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-35 kcal/mol
Surface area14890 Å2
MethodPISA
3
E: CAPSID PROTEIN
F: CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,7182
Polymers34,7182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-31.3 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.790, 67.750, 86.610
Angle α, β, γ (deg.)68.98, 70.75, 84.51
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.0705, 0.9916, 0.1086), (0.9911, -0.0819, 0.1047), (0.1127, 0.1003, -0.9886)-1.3598, -5.82, 60.2134
2given(0.2508, 0.6245, 0.7396), (0.8291, 0.2558, -0.4971), (-0.4996, 0.7379, -0.4537)12.0316, -18.9614, 47.2795
3given(0.8118, 0.3327, -0.4799), (0.1323, 0.6957, 0.7061), (0.5688, -0.6367, 0.5207)-14.7644, 12.7777, 14.5692
4given(0.7783, 0.1416, 0.6117), (0.3426, 0.7206, -0.6028), (-0.5262, 0.6787, 0.5123)-36.2103, 31.306, 53.6832
5given(0.3258, 0.792, -0.5164), (0.6945, 0.1702, 0.6991), (0.6415, -0.5864, -0.4946)33.7575, -37.8837, 6.34

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Components

#1: Protein
CAPSID PROTEIN / CORE ANTIGEN / CORE PROTEIN / HBCAG / P21.5


Mass: 17358.785 Da / Num. of mol.: 6 / Fragment: RESIDUES 1-149 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DISULFIDE LINK BETWEEN C61 RESIDUES AT THE DIMER INTERFACE
Source: (gene. exp.) HEPATITIS B VIRUS / Strain: ADYW / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P03147
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.8 % / Description: NONE
Crystal growTemperature: 293 K / pH: 5.5
Details: 100 MM CITRATE PH 5.0, 15 % (V/V) ISO-PROPANOL, 1% (W/V) PEG 10 000, 293 K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 6, 2013 / Details: TOROIDAL MIRROR (M2)
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→48.69 Å / Num. obs: 24745 / % possible obs: 95.3 % / Observed criterion σ(I): 1.8 / Redundancy: 1.8 % / Biso Wilson estimate: 79.77 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.2
Reflection shellResolution: 3→3.08 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KXS

3kxs


Resolution: 3→44.526 Å / SU ML: 0.5 / σ(F): 1.97 / Phase error: 37.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3173 1260 5.1 %
Rwork0.2521 --
obs0.2555 24741 95.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.54 Å2
Refinement stepCycle: LAST / Resolution: 3→44.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6775 0 0 0 6775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016982
X-RAY DIFFRACTIONf_angle_d1.459569
X-RAY DIFFRACTIONf_dihedral_angle_d14.3172464
X-RAY DIFFRACTIONf_chiral_restr0.0631098
X-RAY DIFFRACTIONf_plane_restr0.0091216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.12030.39281270.35612585X-RAY DIFFRACTION95
3.1203-3.26230.39891480.31822648X-RAY DIFFRACTION96
3.2623-3.43420.33631230.26122674X-RAY DIFFRACTION96
3.4342-3.64930.33231440.25982595X-RAY DIFFRACTION96
3.6493-3.93090.32441430.2472617X-RAY DIFFRACTION95
3.9309-4.32620.31051210.25492626X-RAY DIFFRACTION95
4.3262-4.95150.31131560.25542592X-RAY DIFFRACTION95
4.9515-6.23560.3371410.27682582X-RAY DIFFRACTION95
6.2356-44.53130.28251570.20572562X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 37.4836 Å / Origin y: 2.0907 Å / Origin z: 19.9676 Å
111213212223313233
T0.6018 Å2-0.091 Å2-0.018 Å2-0.6672 Å2-0.0042 Å2--0.7298 Å2
L0.7812 °2-0.9735 °2-0.0107 °2-1.1618 °2-0.408 °2--1.4446 °2
S0.1706 Å °0.2364 Å °0.1715 Å °-0.1862 Å °-0.2081 Å °-0.2038 Å °0.1559 Å °0.0914 Å °-0.0007 Å °
Refinement TLS groupSelection details: ALL

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