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- PDB-4s1l: Structure of Uranotaenia sapphirina cypovirus (CPV17) polyhedrin ... -

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Basic information

Entry
Database: PDB / ID: 4s1l
TitleStructure of Uranotaenia sapphirina cypovirus (CPV17) polyhedrin at 298 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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.752 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 1.1Nov 15, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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

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Assembly

Deposited unit
A: polyhedrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4793
Polymers26,9481
Non-polymers5312
Water3,135174
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 area12010 Å2
ΔGint-77 kcal/mol
Surface area31170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.100, 106.100, 106.100
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

21A-545-

HOH

31A-549-

HOH

41A-558-

HOH

51A-574-

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.: 174 / 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: 5787

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.4 %
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: 298 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.456 Å
DetectorType: Cornell-SLAC Pixel Array Detector (CSPAD) / Detector: FLAT PANEL / Date: Mar 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.456 Å / Relative weight: 1
ReflectionResolution: 1.75→28.3 Å / Num. all: 20140 / Num. obs: 20122 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.75→28.3 Å / % possible all: 100

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Processing

Software
NameVersionClassification
DIALSdata collection
cctbx.xfeldata reduction
PHASERphasing
PHENIX(phenix.refine: dev_1737)refinement
DIALSdata reduction
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.752→28.3 Å / SU ML: 0.21 / σ(F): 1.42 / Phase error: 17.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1543 1032 5.13 %Random
Rwork0.1221 ---
obs0.1238 20122 99.95 %-
all-20140 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.752→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 32 174 2086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011998
X-RAY DIFFRACTIONf_angle_d1.3862721
X-RAY DIFFRACTIONf_dihedral_angle_d14.805757
X-RAY DIFFRACTIONf_chiral_restr0.055282
X-RAY DIFFRACTIONf_plane_restr0.008358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7519-1.84420.2941380.26492713X-RAY DIFFRACTION100
1.8442-1.95970.23081310.17862717X-RAY DIFFRACTION100
1.9597-2.1110.20211710.13832648X-RAY DIFFRACTION100
2.111-2.32330.15771550.11372718X-RAY DIFFRACTION100
2.3233-2.65930.161550.11112719X-RAY DIFFRACTION100
2.6593-3.34960.13231350.11272746X-RAY DIFFRACTION100
3.3496-28.36010.1261470.10712829X-RAY DIFFRACTION100

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