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- PDB-5j2z: PRV UL37 N-terminal half (R2 mutant) -

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Basic information

Entry
Database: PDB / ID: 5j2z
TitlePRV UL37 N-terminal half (R2 mutant)
ComponentsUL37
KeywordsVIRAL PROTEIN / Herpesvirus / Tegument / R2 mutant
Function / homologyHerpesvirus UL37 / Herpesvirus UL37 tegument protein / virion assembly / metal ion binding / ACETATE ION / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / UL37
Function and homology information
Biological speciesSuid herpesvirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHeldwein, E.E. / Pitts, J.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32AI116044 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI056346 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01-NS077003 United States
CitationJournal: PLoS Pathog. / Year: 2017
Title: The pUL37 tegument protein guides alpha-herpesvirus retrograde axonal transport to promote neuroinvasion.
Authors: Richards, A.L. / Sollars, P.J. / Pitts, J.D. / Stults, A.M. / Heldwein, E.E. / Pickard, G.E. / Smith, G.A.
History
DepositionMar 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Apr 13, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_label_seq_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_conn.ptnr2_symmetry
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UL37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,51722
Polymers53,2511
Non-polymers1,26621
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UL37
hetero molecules

A: UL37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,03444
Polymers106,5022
Non-polymers2,53242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+5/21
Buried area9650 Å2
ΔGint-277 kcal/mol
Surface area38020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.281, 68.696, 156.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UL37 / UL37 protein


Mass: 53251.098 Da / Num. of mol.: 1 / Fragment: UNP residues 1-496 / Mutation: Q324A, D362A, R365A, H421A, H425A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suid herpesvirus 1 / Gene: ul37, UL37 / Variant: R2 mutant / Plasmid: PJP55 / Details (production host): R2 mutant in pJP23 plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): T7 Xpress / References: UniProt: Q911W0

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Non-polymers , 7 types, 90 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.4 % / Description: Thin plate-like crystals
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG 1000, 0.3M calcium acetate, 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.48→48.723 Å / Num. obs: 19342 / % possible obs: 96.5 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 14.8
Reflection shellResolution: 2.48→2.54 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 3.5 / % possible all: 67.4

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K70

4k70


Resolution: 2.5→48.723 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 1719 8.94 %Random selection
Rwork0.1781 ---
obs0.1834 19218 96.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3610 0 63 69 3742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073721
X-RAY DIFFRACTIONf_angle_d0.7795066
X-RAY DIFFRACTIONf_dihedral_angle_d14.0792221
X-RAY DIFFRACTIONf_chiral_restr0.043586
X-RAY DIFFRACTIONf_plane_restr0.005672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.57360.28021070.19471093X-RAY DIFFRACTION73
2.5736-2.65660.28811310.19661334X-RAY DIFFRACTION91
2.6566-2.75160.26071460.18431477X-RAY DIFFRACTION99
2.7516-2.86170.26661450.18361479X-RAY DIFFRACTION100
2.8617-2.9920.26761440.19051464X-RAY DIFFRACTION100
2.992-3.14970.24291440.18771468X-RAY DIFFRACTION100
3.1497-3.3470.25671470.18731498X-RAY DIFFRACTION100
3.347-3.60530.24271470.17851495X-RAY DIFFRACTION100
3.6053-3.9680.20431480.15291512X-RAY DIFFRACTION100
3.968-4.54180.22641490.15161505X-RAY DIFFRACTION100
4.5418-5.72080.20731510.17171548X-RAY DIFFRACTION100
5.7208-48.73250.23041600.20191626X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.5259-2.3421-1.0648.6561.89197.20010.336-0.34011.2491-0.6271-0.1171-0.5696-1.275-0.0137-0.20980.4569-0.0830.0410.5007-0.17940.487427.801326.1293219.4875
24.0644-0.1547-0.26514.60612.97496.20450.0815-0.92260.53450.210.0841-0.04230.0411-0.0091-0.0720.1744-0.02780.00920.439-0.07340.256219.88513.4385218.4602
30.76850.70270.81934.3344.63386.09860.0799-0.1578-0.11560.2535-0.0789-0.01460.444-0.1661-0.00210.2383-0.0287-0.0060.27020.04630.187413.8921-1.6358198.2462
43.6934-0.86351.41523.03580.37724.07230.17230.3958-0.421-0.0172-0.0719-0.21690.67970.493-0.03150.39070.03040.00090.2556-0.04010.2916.4152-17.8995171.116
50.9308-0.56260.51971.460.98966.1175-0.01810.0556-0.0139-0.03350.0741-0.0571-0.1551-0.0706-0.02830.1308-0.0260.00750.17770.01690.19217.84374.6292178.4344
63.3744-0.008-0.00766.38335.52478.44230.1187-0.15961.2298-0.53520.0087-0.3403-1.3695-0.0232-0.02610.59650.10460.02290.4703-0.10350.691110.315426.317212.2559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 133 )
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 197 )
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 316 )
5X-RAY DIFFRACTION5chain 'A' and (resid 317 through 432 )
6X-RAY DIFFRACTION6chain 'A' and (resid 433 through 477 )

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