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- PDB-5ed7: Crystal Structure of HSV-1 UL21 C-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 5ed7
TitleCrystal Structure of HSV-1 UL21 C-terminal Domain
ComponentsTegument protein UL21
KeywordsVIRAL PROTEIN
Function / homologyHerpesvirus UL21 / Herpesvirus UL21 / viral tegument / host cell cytoplasm / host cell nucleus / Tegument protein UL21
Function and homology information
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.72 Å
AuthorsMetrick, C.M. / Heldwein, E.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31 GM115121 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR029205 United States
CitationJournal: J.Virol. / Year: 2016
Title: Novel Structure and Unexpected RNA-Binding Ability of the C-Terminal Domain of Herpes Simplex Virus 1 Tegument Protein UL21.
Authors: Metrick, C.M. / Heldwein, E.E.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tegument protein UL21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5697
Polymers27,3561
Non-polymers2136
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.273, 54.273, 180.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Tegument protein UL21


Mass: 27356.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (strain 17) / Strain: 17 / Gene: UL21 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21(DE3) / References: UniProt: P10205
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, sodium citrate, NDSB 256, sodium fluoride
PH range: 3.5-4.0 / Temp details: ambient

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 15, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 50.6 % / Number: 371602 / Rsym value: 0.181 / D res high: 2.876 Å / D res low: 185.082 Å / Num. obs: 7347 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
9.1185.0810.0680.06838
6.449.110.0690.06946.7
5.256.4410.1170.11753.2
4.555.2510.1510.15149.9
4.074.5510.1990.19954.3
3.724.0710.3510.35152.6
3.443.7210.5650.56553.9
3.223.4410.9550.95556.4
3.033.2211.6271.62753.8
2.883.0312.4812.48139.8
ReflectionResolution: 2.72→54.27 Å / Num. obs: 7854 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 71.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.029 / Net I/σ(I): 20.6 / Num. measured all: 52609
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.72-2.857.20.9232.4717310020.7590.36499.7
9.02-54.275.20.01866.5138926610.00899.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
SCALA0.1.27data scaling
SHELXphasing
RESOLVEmodel building
Cootmodel building
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.72→51.98 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 360 4.61 %
Rwork0.2177 --
obs0.2184 7813 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.72→51.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 6 2 1941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021977
X-RAY DIFFRACTIONf_angle_d0.4082690
X-RAY DIFFRACTIONf_dihedral_angle_d8.5551181
X-RAY DIFFRACTIONf_chiral_restr0.036303
X-RAY DIFFRACTIONf_plane_restr0.004351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-3.11360.32211050.27772409X-RAY DIFFRACTION100
3.1136-3.92260.27261340.23812440X-RAY DIFFRACTION100
3.9226-51.98990.20041210.19722604X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 48.5178 Å / Origin y: 12.235 Å / Origin z: 74.5435 Å
111213212223313233
T0.5763 Å2-0.0131 Å2-0.009 Å2-0.388 Å20.0039 Å2--0.5255 Å2
L2.7569 °2-1.7509 °2-0.3735 °2-2.0587 °20.5455 °2--3.4024 °2
S-0.257 Å °-0.1324 Å °0.0467 Å °0.2973 Å °0.1467 Å °-0.1655 Å °0.0572 Å °0.3141 Å °0.1266 Å °
Refinement TLS groupSelection details: all

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