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- PDB-2qij: Hepatitis B Capsid Protein with an N-terminal extension modelled ... -

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Basic information

Entry
Database: PDB / ID: 2qij
TitleHepatitis B Capsid Protein with an N-terminal extension modelled into 8.9 A data.
ComponentsCore antigen
KeywordsVIRUS / VIRAL CAPSID PROTEIN / icosahedral virus
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 core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
Biological speciesHepatitis B virus subtype adyw
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 8.9 Å
AuthorsTan, W.S. / McNae, I.W. / Ho, K.L. / Walkinshaw, M.D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and X-ray analysis of the T = 4 particle of hepatitis B capsid protein with an N-terminal extension.
Authors: Tan, W.S. / McNae, I.W. / Ho, K.L. / Walkinshaw, M.D.
History
DepositionJul 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: refine / Item: _refine.ls_percent_reflns_obs
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Core antigen
D: Core antigen
B: Core antigen
A: Core antigen


Theoretical massNumber of molelcules
Total (without water)70,9854
Polymers70,9854
Non-polymers00
Water00
1
C: Core antigen
D: Core antigen
B: Core antigen
A: Core antigen
x 60


Theoretical massNumber of molelcules
Total (without water)4,259,102240
Polymers4,259,102240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Core antigen
D: Core antigen
B: Core antigen
A: Core antigen
x 5


  • icosahedral pentamer
  • 355 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)354,92520
Polymers354,92520
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
C: Core antigen
D: Core antigen
B: Core antigen
A: Core antigen
x 6


  • icosahedral 23 hexamer
  • 426 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)425,91024
Polymers425,91024
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
C: Core antigen
D: Core antigen
B: Core antigen
A: Core antigen
x 60


  • crystal asymmetric unit, crystal frame
  • 4.26 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)4,259,102240
Polymers4,259,102240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)352.318, 465.522, 645.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.50549993, -0.82901251, -0.23918209), (0.77376709, 0.31290036, 0.55079748), (-0.38177785, -0.46349931, 0.7996337)-21.76898, 51.66872, -18.37305
3generate(-0.294618, -0.56760335, -0.76878259), (0.42296893, -0.79885022, 0.42770973), (-0.85691162, -0.19916016, 0.47543423)-71.21271, 40.87194, -48.70226
4generate(-0.294618, 0.42296892, -0.85691162), (-0.56760335, -0.79885022, -0.19916016), (-0.76878259, 0.42770974, 0.47543423)-80.00164, -17.46956, -49.0737
5generate(0.50549992, 0.77376708, -0.38177785), (-0.82901252, 0.31290036, -0.46349931), (-0.23918209, 0.55079748, 0.79963371)-35.98976, -42.72981, -18.97404
6generate(-0.83951886, -0.31557025, -0.44229346), (-0.31557025, -0.37946241, 0.86972622), (-0.44229347, 0.86972622, 0.21898126)56.29426, 214.49909, -132.6164
7generate(-0.49969675, 0.80223231, -0.32669019), (-0.78517847, -0.26023974, 0.56193421), (0.36578401, 0.5373068, 0.75993649)66.39089, 185.78288, -82.07383
8generate(0.49286736, 0.81669431, 0.30015356), (-0.81280664, 0.30903755, 0.49380276), (0.31052719, -0.48734607, 0.81612908)124.72139, 179.10471, -76.23697
9generate(0.76648361, -0.29217024, 0.57196103), (-0.36027357, 0.54164759, 0.75948722), (-0.53170088, -0.78819695, 0.30990278)150.67499, 203.69359, -123.17216
10generate(-0.05697636, -0.99194822, 0.11310353), (-0.05296458, 0.11613122, 0.9918207), (-0.99696964, 0.05051985, -0.05915486)108.38469, 225.56853, -158.01656
11generate(-0.38181678, 0.84358927, -0.3775885), (0.84358928, 0.15118438, -0.51526733), (-0.37758851, -0.51526733, -0.7693676)44.54923, -205.13853, -385.37476
12generate(0.60388819, 0.75550228, 0.25403809), (0.74013347, -0.41321437, -0.53052459), (-0.29584035, 0.50839962, -0.8087078)103.38562, -206.22407, -389.64262
13generate(0.79286212, -0.38198041, 0.47482694), (0.25694827, -0.49697705, -0.82884944), (0.55258234, 0.77916929, -0.29588507)124.60797, -233.93893, -342.0757
14generate(-0.07605053, -0.99689639, -0.02034464), (0.0617792, 0.01565352, -0.99796708), (0.99518825, -0.0771528, 0.06039701)78.88772, -249.98211, -308.40986
15generate(-0.80204202, -0.23945267, -0.54716636), (0.42434329, 0.41623931, -0.80416268), (0.42031105, -0.87715862, -0.23223129)29.40869, -232.18248, -335.17015
16generate(0.22133564, -0.52801902, 0.81988197), (-0.52801903, -0.77172197, -0.35445889), (0.81988197, -0.35445889, -0.44961366)254.0787, -56.88749, -415.12444
17generate(-0.60969137, -0.72872208, 0.31183419), (-0.72872209, 0.36055375, -0.58220711), (0.31183419, -0.58220711, -0.75086239)206.91465, -78.75445, -443.0261
18generate(-0.99111149, 0.13288945, -0.00619791), (0.13288944, 0.98678972, -0.09266305), (-0.00619791, -0.09266306, -0.99567823)176.80552, -33.56465, -466.10068
19generate(-0.39581508, 0.86609771, 0.30529523), (0.86609771, 0.24154911, 0.43764002), (0.30529523, 0.43764001, -0.84573402)205.36111, 16.23115, -452.45989
20generate(0.35351845, 0.45763381, 0.81584067), (0.45763382, -0.84527089, 0.27584129), (0.81584067, 0.27584129, -0.50824756)253.11856, 1.81684, -420.95485
21generate(0.81330204, -0.40820208, -0.41462135), (0.18749056, -0.49072689, 0.85090212), (-0.55080586, -0.76977801, -0.32257515)-85.00675, 164.14895, -268.80187
22generate(0.25356403, -0.60978743, -0.75090916), (-0.60978743, -0.70337318, 0.36527449), (-0.75090916, 0.3652745, -0.55019085)-116.18492, 119.07858, -290.65815
23generate(-0.05697636, -0.05296458, -0.99696963), (-0.99194823, 0.11613122, 0.05051985), (0.11310353, 0.99182069, -0.05915486)-139.4152, 89.29943, -245.32967
24generate(0.31083712, 0.49275621, -0.81275555), (-0.43085861, 0.83525908, 0.3416184), (0.84719605, 0.24399504, 0.47193779)-122.59413, 115.96528, -195.45886
25generate(0.84869875, 0.27320737, -0.45284452), (0.29807465, 0.46020014, 0.83628185), (0.43687748, -0.84473283, 0.30913509)-88.96785, 162.22483, -209.96547
26generate(-0.37058165, -0.46236364, -0.80553653), (-0.3788915, 0.86709785, -0.32339227), (0.84800382, 0.1853677, -0.4965162)-71.7959, -43.40045, -422.14701
27generate(-0.23755476, 0.5359087, -0.8101664), (0.60286616, 0.73531311, 0.30962401), (0.76165618, -0.41486925, -0.49775835)-72.8183, 15.59117, -421.90695
28generate(0.60388819, 0.74013346, -0.29584035), (0.75550229, -0.41321437, 0.50839962), (0.25403809, -0.53052459, -0.8087078)-25.07203, 34.77134, -450.77786
29generate(0.99090164, -0.13192104, 0.0266605), (-0.13192104, -0.99125865, -0.00176658), (0.0266605, -0.00176658, -0.99964298)5.45918, -12.36628, -468.86111
30generate(0.38864616, -0.87510512, -0.28834907), (-0.83301496, -0.19998219, -0.51584224), (0.39375151, 0.44067919, -0.80669796)-23.41776, -60.6791, -451.16627
31generate(-0.498331, 0.83801993, 0.22223592), (-0.80684984, -0.35446728, -0.47259527), (-0.31726889, -0.41481989, 0.85279828)194.74781, -54.74769, -11.11639
32generate(0.3116812, 0.57233318, 0.75847845), (-0.50171125, 0.77702326, -0.38015876), (-0.80693287, -0.26204883, 0.52932953)244.81223, -46.81525, -41.31149
33generate(0.31083713, -0.4308586, 0.84719605), (0.49275622, 0.83525908, 0.24399504), (-0.81275556, 0.3416184, 0.47193778)253.66341, 11.23896, -47.01051
34generate(-0.49969674, -0.78517846, 0.36578401), (0.80223232, -0.26023974, 0.5373068), (-0.32669019, 0.56193421, 0.75993649)209.06932, 39.186, -20.3376
35generate(-0.99979015, -0.0009684, -0.02046259), (-0.0009684, -0.99553107, 0.09442963), (-0.02046259, 0.09442964, 0.99532122)172.65747, -1.596, 1.84618
36generate(0.05561062, 0.03254579, 0.99792195), (0.99825078, -0.02190368, -0.05491458), (0.02007092, 0.9992302, -0.03370694)316.97702, -113.52773, -231.05034
37generate(-0.32769047, -0.49845445, 0.8025971), (0.50863252, -0.80896319, -0.29473975), (0.79618586, 0.31164358, 0.51861967)299.11317, -135.38142, -179.23901
38generate(-0.85774895, -0.25631028, 0.44561393), (-0.25631028, -0.53817593, -0.80291451), (0.44561394, -0.80291451, 0.39592488)265.74599, -182.83666, -189.99756
39generate(-0.80204202, 0.42434329, 0.42031105), (-0.23945267, 0.41623931, -0.87715862), (-0.54716636, -0.80416267, -0.23223129)262.9878, -190.31192, -248.45804
40generate(-0.23755476, 0.60286615, 0.76165618), (0.53590871, 0.73531311, -0.41486924), (-0.8101664, 0.30962401, -0.49775835)294.65032, -147.47665, -273.83005
41generate(0.81330203, 0.18749055, -0.55080586), (-0.40820208, -0.49072689, -0.76977801), (-0.41462135, 0.85090212, -0.32257514)-109.69786, -161.06539, -261.62911
42generate(0.76648361, -0.36027357, -0.53170088), (-0.29217025, 0.54164759, -0.78819695), (0.57196103, 0.75948722, 0.30990279)-107.59523, -163.39131, -202.71151
43generate(0.3116812, -0.50171124, -0.80693287), (0.57233318, 0.77702326, -0.26204883), (0.75847846, -0.38015876, 0.52932953)-133.12671, -114.56325, -181.61464
44generate(0.07741627, -0.04136041, -0.99614057), (0.99059384, -0.10988106, 0.08154753), (-0.11282982, -0.99308382, 0.03246479)-151.00865, -82.05992, -227.49365
45generate(0.387435, 0.38458972, -0.83784537), (0.38458973, -0.89339374, -0.23224636), (-0.83784537, -0.23224635, -0.49404126)-136.52883, -110.79983, -276.94531
46generate(-0.498331, -0.80684984, -0.31726889), (0.83801993, -0.35446728, -0.41481989), (0.22223593, -0.47259526, 0.85279828)49.34882, -187.22011, -59.67342
47generate(-0.7550939, 0.30771295, -0.57891791), (0.30771295, -0.61337322, -0.72738301), (-0.57891791, -0.72738301, 0.36846712)24.33727, -216.15631, -104.59816
48generate(0.07741627, 0.99059383, -0.11282982), (-0.04136041, -0.10988106, -0.99308382), (-0.99614057, 0.08154754, 0.03246479)67.31051, -241.18288, -136.34853
49generate(0.84869875, 0.29807465, 0.43687748), (0.27320737, 0.46020014, -0.84473283), (-0.45284453, 0.83628185, 0.3091351)118.88098, -227.71394, -111.04659
50generate(0.49286737, -0.81280663, 0.31052719), (0.81669432, 0.30903754, -0.48734607), (0.30015356, 0.49380276, 0.81612908)107.78005, -194.36312, -63.65876
51generate(0.05561062, 0.99825077, 0.02007093), (0.03254579, -0.02190368, 0.99923021), (0.99792196, -0.05491459, -0.03370694)100.33926, 218.06953, -330.34066
52generate(0.79286212, 0.25694827, 0.55258234), (-0.38198041, -0.49697705, 0.77916929), (0.47482694, -0.82884944, -0.29588507)150.33825, 197.87041, -354.28246
53generate(0.38864616, -0.83301495, 0.39375151), (-0.87510513, -0.19998218, 0.44067919), (-0.28834907, -0.51584224, -0.80669796)136.20202, 166.19185, -402.00824
54generate(-0.59842455, -0.76534676, -0.23692276), (-0.76534676, 0.4586441, 0.45154172), (-0.23692276, 0.45154172, -0.86021955)77.46635, 166.81255, -407.56259
55generate(-0.80425184, 0.3664377, -0.46787006), (-0.20438765, 0.56870267, 0.79674523), (0.55803645, 0.73641067, -0.38248483)55.30195, 198.87472, -363.26958
56generate(-0.37058165, -0.37889149, 0.84800382), (-0.46236365, 0.86709785, 0.1853677), (-0.80553653, -0.32339227, -0.4965162)314.93197, 82.68904, -281.47242
57generate(-0.80425183, -0.20438764, 0.55803645), (0.36643771, 0.56870267, 0.73641067), (-0.46787007, 0.79674523, -0.38248483)287.8419, 134.1503, -271.52346
58generate(-0.77774363, 0.34413236, 0.52601118), (0.34413236, -0.46716001, 0.81445346), (0.52601118, 0.81445346, 0.24490364)284.53636, 142.02736, -213.14419
59generate(-0.32769047, 0.50863252, 0.79618585), (-0.49845445, -0.80896319, 0.31164358), (0.80259711, -0.29473975, 0.51861967)309.58349, 95.43439, -187.01277
60generate(-0.07605053, 0.06177921, 0.99518824), (-0.99689639, 0.01565352, -0.0771528), (-0.02034464, -0.99796708, 0.06039701)328.36901, 58.7613, -229.24194

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Components

#1: Protein
Core antigen


Mass: 17746.258 Da / Num. of mol.: 4 / Fragment: Hepatitis B Capsid Protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus subtype adyw / Genus: Orthohepadnavirus / Species: Hepatitis B virus / Strain: subtype adyw / Gene: C / Production host: Escherichia coli (E. coli) / References: UniProt: P03147

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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: 7.8 Å3/Da / Density % sol: 84 %
Crystal growMethod: vapor diffusion, hanging drop / Details: 11-14% MPD, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 8.9→60.41 Å / Num. all: 81623 / Num. obs: 81623 / % possible obs: 99.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.219 / Net I/σ(I): 7.1
Reflection shellResolution: 8.9→9.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QGT

1qgt


Resolution: 8.9→60.41 Å / Num. reflection obs: 81623
Refinement stepCycle: LAST / Resolution: 8.9→60.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4625 0 0 0 4625

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