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- PDB-4u4h: Crystal Structure of HSV-1 UL21 N-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 4u4h
TitleCrystal Structure of HSV-1 UL21 N-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: 2.05 Å
Model detailsStrepII affinity tag and residues 1-198
AuthorsMetrick, C.M. / Heldwein, E.E.
CitationJournal: J.Virol. / Year: 2015
Title: The Unusual Fold of Herpes Simplex Virus 1 UL21, a Multifunctional Tegument Protein.
Authors: Metrick, C.M. / Chadha, P. / Heldwein, E.E.
History
DepositionJul 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / software
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.d_res_high / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _software.pdbx_ordinal

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tegument protein UL21


Theoretical massNumber of molelcules
Total (without water)23,1801
Polymers23,1801
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Tegument protein UL21

A: Tegument protein UL21


Theoretical massNumber of molelcules
Total (without water)46,3612
Polymers46,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2850 Å2
ΔGint-3 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.346, 108.346, 65.236
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Tegument protein UL21


Mass: 23180.256 Da / Num. of mol.: 1 / Fragment: N-terminal domain (1-198)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Strain: 17 / Gene: UL21 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21(DE3) / References: UniProt: P10205
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ammonium Sulfate, HEPES, 2-methyl-2,4-pentanediol / Temp details: ambient

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2013
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→41.7 Å / Num. obs: 14650 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 35.18 Å2 / Rmerge(I) obs: 0.06077 / Rsym value: 0.06772 / Net I/σ(I): 23.3
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SHARPphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.05→30.809 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 713 5.01 %
Rwork0.1655 13512 -
obs0.1683 14225 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.87 Å2 / Biso mean: 51.3727 Å2 / Biso min: 26.32 Å2
Refinement stepCycle: final / Resolution: 2.05→30.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 0 66 1611
Biso mean---49.36 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071615
X-RAY DIFFRACTIONf_angle_d1.0752204
X-RAY DIFFRACTIONf_chiral_restr0.079251
X-RAY DIFFRACTIONf_plane_restr0.005289
X-RAY DIFFRACTIONf_dihedral_angle_d12.552587
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.20740.26961290.1982498262792
2.2074-2.42940.25691400.18882610275096
2.4294-2.78080.25331430.19772693283698
2.7808-3.50270.2231480.17962771291999
3.5027-30.8130.19731530.142429403093100
Refinement TLS params.Method: refined / Origin x: -65.986 Å / Origin y: 4.4918 Å / Origin z: 11.0558 Å
111213212223313233
T0.2404 Å20.0349 Å20.0059 Å2-0.2668 Å2-0.0615 Å2--0.2163 Å2
L2.0643 °20.6631 °2-0.0915 °2-4.2882 °2-0.1883 °2--3.0697 °2
S0.0396 Å °-0.1376 Å °0.0379 Å °0.1509 Å °-0.0878 Å °0.1781 Å °-0.064 Å °-0.3287 Å °0.021 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-10 - 198
2X-RAY DIFFRACTION1allS1 - 56
3X-RAY DIFFRACTION1allS57 - 67

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