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- PDB-4s1k: Structure of Uranotaenia sapphirina cypovirus (CPV17) polyhedrin ... -

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Basic information

Entry
Database: PDB / ID: 4s1k
TitleStructure of Uranotaenia sapphirina cypovirus (CPV17) polyhedrin at 100 K
ComponentsPolyhedrin
KeywordsVIRAL PROTEIN / Polyhedrin
Function / homologyCypovirus polyhedrin / Cypovirus polyhedrin / ATP binding / ADENOSINE-5'-TRIPHOSPHATE / Polyhedrin
Function and homology information
Biological speciesUranotaenia sapphirina cypovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGinn, H.M. / Messerschmidt, M. / Ji, X. / Zhang, H. / Axford, D. / Gildea, R.J. / Winter, G. / Brewster, A.S. / Hattne, J. / Wagner, A. ...Ginn, H.M. / Messerschmidt, M. / Ji, X. / Zhang, H. / Axford, D. / Gildea, R.J. / Winter, G. / Brewster, A.S. / Hattne, J. / Wagner, A. / Grimes, J.M. / Evans, G. / Sauter, N.K. / Sutton, G. / Stuart, D.I.
CitationJournal: Nat Commun / Year: 2015
Title: Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data.
Authors: Ginn, H.M. / Messerschmidt, M. / Ji, X. / Zhang, H. / Axford, D. / Gildea, R.J. / Winter, G. / Brewster, A.S. / Hattne, J. / Wagner, A. / Grimes, J.M. / Evans, G. / Sauter, N.K. / Sutton, G. / Stuart, D.I.
History
DepositionJan 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyhedrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4793
Polymers26,9481
Non-polymers5312
Water2,630146
1
A: Polyhedrin
hetero molecules

A: Polyhedrin
hetero molecules

A: Polyhedrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4379
Polymers80,8433
Non-polymers1,5946
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
Buried area11870 Å2
ΔGint-76 kcal/mol
Surface area31180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.879, 104.879, 104.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-532-

HOH

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Components

#1: Protein Polyhedrin


Mass: 26947.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Uranotaenia sapphirina cypovirus / References: UniProt: Q5EK29
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 768

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Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 31.04 %
Crystal growTemperature: 301 K / Method: in vivo / pH: 7.5
Details: CRYSTALS FORMED NATURALLY WITHIN THE CYTOPLASM AND WERE PURIFIED FROM CELLS, pH 7.5, In vivo, temperature 301K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2014
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.2→74 Å / Num. all: 9903 / Num. obs: 9376 / % possible obs: 99.79 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→74.16 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
DIALSdata collection
PHASERphasing
REFMAC5.8.0049refinement
DIALSdata reduction
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→74 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.984 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 1.2 / ESU R: 0.478 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19892 504 5.1 %RANDOM
Rwork0.14771 ---
obs0.15054 9376 99.79 %-
all-9376 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.242 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1881 0 32 146 2059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191996
X-RAY DIFFRACTIONr_bond_other_d0.0010.021832
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.9692715
X-RAY DIFFRACTIONr_angle_other_deg0.85434214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6075242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31623.63699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40215331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4541517
X-RAY DIFFRACTIONr_chiral_restr0.0940.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02482
X-RAY DIFFRACTIONr_mcbond_it1.4162.12962
X-RAY DIFFRACTIONr_mcbond_other1.4122.12961
X-RAY DIFFRACTIONr_mcangle_it2.273.1741206
X-RAY DIFFRACTIONr_mcangle_other2.2693.1741207
X-RAY DIFFRACTIONr_scbond_it2.1532.4441034
X-RAY DIFFRACTIONr_scbond_other2.1522.4461035
X-RAY DIFFRACTIONr_scangle_other3.3323.5791510
X-RAY DIFFRACTIONr_long_range_B_refined5.53218.1772325
X-RAY DIFFRACTIONr_long_range_B_other5.35618.0422295
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 32 -
Rwork0.251 676 -
obs--100 %

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