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- PDB-2e0z: Crystal structure of virus-like particle from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 2e0z
TitleCrystal structure of virus-like particle from Pyrococcus furiosus
ComponentsVirus-like particle
KeywordsVIRUS LIKE PARTICLE / virus-like particle / virus / bacteriophage / HK97 / T4
Function / homology
Function and homology information


peptidase activity / oxidoreductase activity / defense response to bacterium / metal ion binding
Similarity search - Function
Major capsid protein gp5 fold - #20 / Rhinovirus 14, subunit 4 - #90 / hypothetical protein PF0899 domain / Major capsid protein gp5 fold / Rhinovirus 14, subunit 4 / hypothetical protein PF0899 fold / Rubrerythrin, diiron-binding domain / Rubrerythrin / Type 1 encapsulin shell protein / Encapsulating protein for peroxidase ...Major capsid protein gp5 fold - #20 / Rhinovirus 14, subunit 4 - #90 / hypothetical protein PF0899 domain / Major capsid protein gp5 fold / Rhinovirus 14, subunit 4 / hypothetical protein PF0899 fold / Rubrerythrin, diiron-binding domain / Rubrerythrin / Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / Other non-globular / Ferritin-like / Ferritin-like superfamily / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.6 Å
AuthorsAkita, F. / Chong, K.T. / Tanaka, H. / Yamashita, E. / Miyazaki, N. / Nakaishi, Y. / Namba, K. / Ono, Y. / Suzuki, M. / Tsukihara, T. / Nakagawa, A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Crystal Structure of a Virus-like Particle from the Hyperthermophilic Archaeon Pyrococcus furiosus Provides Insight into the Evolution of Viruses
Authors: Akita, F. / Chong, K.T. / Tanaka, H. / Yamashita, E. / Miyazaki, N. / Nakaishi, Y. / Suzuki, M. / Namba, K. / Ono, Y. / Tsukihara, T. / Nakagawa, A.
History
DepositionOct 16, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
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
Remark 295 REMARK: THE SUPPLIED NCS OPERATORS AND THE IDENTITY MATRIX ARE SUFFICIENT TO GENERATE HALF OF THE ... REMARK: THE SUPPLIED NCS OPERATORS AND THE IDENTITY MATRIX ARE SUFFICIENT TO GENERATE HALF OF THE PARTICLE (30 COPIES OF THE BIOLOGICAL ASYMMETRIC UNIT). THE BIOLOGICAL ASYMMETRIC UNIT IS COMPOSED OF THREE CHAINS, A, B, and C.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Virus-like particle
B: Virus-like particle
C: Virus-like particle


Theoretical massNumber of molelcules
Total (without water)116,5493
Polymers116,5493
Non-polymers00
Water0
1
A: Virus-like particle
B: Virus-like particle
C: Virus-like particle
x 60


Theoretical massNumber of molelcules
Total (without water)6,992,957180
Polymers6,992,957180
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
A: Virus-like particle
B: Virus-like particle
C: Virus-like particle
x 5


  • icosahedral pentamer
  • 583 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)582,74615
Polymers582,74615
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Virus-like particle
B: Virus-like particle
C: Virus-like particle
x 6


  • icosahedral 23 hexamer
  • 699 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)699,29618
Polymers699,29618
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
Unit cell
Length a, b, c (Å)631.500, 631.500, 351.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-0.11224, 0.92998999, 0.35001999), (-0.46176001, -0.36072001, 0.81033999), (0.87987, -0.07067, 0.46992999)-39.94495, 67.505, -0.64422
3generate(-0.11695, -0.47049001, 0.87462002), (0.93052, -0.35968, -0.06906), (0.34707999, 0.80576998, 0.47986999)28.02007, 61.27095, -40.79925
4generate(0.36521, -0.92699999, -0.0854), (0.82275999, 0.36432999, -0.43626001), (0.43553001, 0.08906, 0.89576)195.65263, 56.16118, -41.70843
5generate(0.30928001, 0.67416, -0.67071998), (-0.65398002, 0.66281998, 0.36465999), (0.69041002, 0.32585001, 0.64587998)119.34791, 49.33548, -54.19053
6generate(-0.93427998, 0.09372, 0.34401), (0.09214, -0.86860001, 0.48688), (0.34443, 0.48657, 0.80287999)152.56224, 119.21985, -60.61504
7generate(0.30678001, -0.65171999, 0.69365001), (0.67359, 0.66355002, 0.32552999), (-0.67242998, 0.36737001, 0.64256001)32.93805, -95.39608, 97.34435
8generate(0.87702, 0.47137001, -0.09296), (-0.10126, 0.37049001, 0.92330003), (0.46966001, -0.80034, 0.37266001)-23.83386, -77.61978, 148.25436
9generate(-0.39897001, 0.65305001, 0.6437), (0.65307999, -0.2904, 0.69940001), (0.64367002, 0.69941998, -0.31062999)-26.81414, -49.2828, 75.28936
10generate(0.34876001, 0.81309998, 0.46608001), (-0.93147999, 0.35565001, 0.07657), (-0.1035, -0.46085, 0.88142002)-98.13868, 166.13696, 82.43605
11generate(-0.02191, 0.02664, 0.99940997), (0.01404, -0.99953997, 0.02695), (0.99966002, 0.01462, 0.02152)-58.54097, 225.82253, 53.70372
12generate(0.87616998, -0.10041, 0.47143), (0.47268, 0.3705, -0.79956001), (-0.09438, 0.92338997, 0.37209001)-56.59997, 158.5694, 14.5729
13generate(0.66209, 0.30923, 0.68265003), (0.67457998, -0.64270997, -0.36313), (0.32646, 0.70093, -0.63413)-114.45999, 177.33109, 170.48409
14generate(0.37547001, 0.48745, 0.78829998), (-0.10617, 0.86755002, -0.48589), (-0.92072999, 0.09874, 0.37749001)-121.60933, 110.12406, 205.54401
15generate(0.43742999, 0.12777001, 0.89012998), (-0.80830997, -0.3779, 0.45146), (0.39407, -0.91698998, -0.06203)-105.22178, 172.37025, 248.16454
16generate(0.44275001, -0.80800998, 0.38870999), (0.12225, -0.37507001, -0.91890001), (0.88827002, 0.45436999, -0.06728)89.34673, 306.24875, 32.59674
17generate(0.66505998, 0.67499, -0.3195), (-0.64826, 0.30941001, -0.69572002), (-0.37075001, 0.66982001, 0.64335001)17.09513, 276.76471, 28.01223
18generate(-0.66802001, 0.39932001, 0.62792999), (-0.68239999, -0.66526002, -0.30291), (0.29677999, -0.63085002, 0.71689999)36.38606, 324.03168, 87.65511
19generate(-0.45383, 0.79636002, -0.39980999), (-0.88572001, -0.45231, 0.10448), (-0.09763, 0.40153, 0.91062999)146.44136, 252.1656, -18.90988
20generate(0.65253001, -0.40022001, -0.64345002), (-0.28573, 0.65651, -0.69810998), (0.70183003, 0.63938999, 0.31404001)198.90974, 196.04793, -34.10129
21generate(-0.66746998, -0.68344998, 0.29559001), (0.40301999, -0.66536999, -0.62836999), (0.62614, -0.30028999, 0.71956998)218.62607, 256.70502, 11.67351
22generate(-0.33792999, -0.67917001, 0.65154999), (-0.66216999, -0.32038999, -0.67741001), (0.66882998, -0.66035998, -0.34145999)115.58798, 346.65933, 235.01936
23generate(0.92956001, -0.11643, -0.34981), (-0.36162001, -0.47279, -0.80356002), (-0.07183, 0.87344998, -0.48159)82.12108, 352.44669, 165.51663
24generate(-0.35905999, 0.93106002, 0.06491), (-0.45839, -0.11534, -0.88124001), (-0.81299001, -0.34617001, 0.4682)37.60475, 336.10419, 226.91467
25generate(0.47402999, 0.87434, 0.10403), (0.37443, -0.09323, -0.92255998), (-0.79693002, 0.47626999, -0.37156999)-57.10955, 246.13786, 278.63669
26generate(-0.37990001, 0.11616, 0.91771001), (-0.80557001, 0.4461, -0.38993999), (-0.45468, -0.88740999, -0.0759)-16.12032, 225.52826, 343.04987
27generate(0.79459, -0.4585, 0.398), (-0.45831001, -0.88291001, -0.10213), (0.39822, -0.10126, -0.91167998)6.1072, 288.01407, 301.30505
28generate(-0.99988002, 0.01451, -0.00608), (0.00549, -0.03999, -0.99918002), (-0.01474, -0.99909002, 0.03991)231.26413, 292.6561, 286.77707
29generate(0.09869, -0.93466997, -0.34154999), (-0.86568999, 0.08863, -0.49267), (0.49075001, 0.3443, -0.80039001)272.28351, 290.77356, 220.55716
30generate(0.13465001, 0.45376, -0.88089001), (-0.35736001, -0.80693001, -0.47027999), (-0.92421001, 0.37812001, 0.0535)204.43503, 330.92676, 226.25446

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Components

#1: Protein Virus-like particle /


Mass: 38849.762 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q401P1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 46

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Sample preparation

Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5 / Details: 16~20% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONSPring-8 BL44XU20.9
Detector
TypeIDDetectorDate
Bruker DIP-60401CCDJun 11, 2004
Bruker DIP-60402CCDDec 15, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.6→20 Å / Num. obs: 773334 / % possible obs: 96.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 104 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 8.8
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 1.6 / % possible all: 97.5

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Processing

Software
NameClassification
HKL-2000data collection
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.6→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.267 -5 %RANDOM
Rwork0.268 ---
obs-773334 --
Displacement parametersBiso mean: 100 Å2
Refinement stepCycle: LAST / Resolution: 3.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5488 0 0 0 5488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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