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- PDB-3n4p: Human cytomegalovirus terminase nuclease domain -

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Basic information

Entry
Database: PDB / ID: 3n4p
TitleHuman cytomegalovirus terminase nuclease domain
ComponentsTerminase subunit UL89 protein
KeywordsDNA BINDING PROTEIN / Terminase / Nuclease / Human cytomegalovirus / HCMV / herpesvirus / DNA packaging
Function / homology
Function and homology information


chromosome organization / Hydrolases; Acting on ester bonds / hydrolase activity / host cell nucleus / DNA binding
Similarity search - Function
DNA-packaging terminase, C-terminal nuclease domain / Probable DNA packing protein, C-terminal / Probable DNA packing protein, N-terminal / Tripartite terminase subunit 3 / Probable DNA packing protein, C-terminal domain superfamily / Probable DNA packing protein, C-terminus / Probable DNA packing protein, N-terminus / Nucleotidyltransferase; domain 5 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tripartite terminase subunit 3
Similarity search - Component
Biological speciesHuman herpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.15 Å
AuthorsNadal, M. / Mas, P.J. / Blanco, A.G. / Arnan, C. / Sola, M. / Hart, D.J. / Coll, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure and inhibition of herpesvirus DNA packaging terminase nuclease domain.
Authors: Nadal, M. / Mas, P.J. / Blanco, A.G. / Arnan, C. / Sola, M. / Hart, D.J. / Coll, M.
History
DepositionMay 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_ref_seq_dif / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_label_seq_id / _struct_ref_seq_dif.details / _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: Terminase subunit UL89 protein
B: Terminase subunit UL89 protein
C: Terminase subunit UL89 protein
D: Terminase subunit UL89 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,44211
Polymers127,2724
Non-polymers1707
Water1,76598
1
A: Terminase subunit UL89 protein
B: Terminase subunit UL89 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7095
Polymers63,6362
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-26 kcal/mol
Surface area21380 Å2
MethodPISA
2
C: Terminase subunit UL89 protein
D: Terminase subunit UL89 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7336
Polymers63,6362
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-30 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.860, 87.960, 188.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE DIMER IS NOT FUNCTIONALLY CONFIRMED

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Components

#1: Protein
Terminase subunit UL89 protein


Mass: 31817.889 Da / Num. of mol.: 4 / Fragment: unp residues 418-674
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 / Strain: Towne / Plasmid: pHAR / Production host: Escherichia coli (E. coli) / References: UniProt: P16732
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 58.59 %

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-211
SYNCHROTRONESRF ID14-421.00726
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.007261
ReflectionResolution: 2.15→98.7 Å / Num. obs: 72855 / % possible obs: 96.3 % / Redundancy: 6 % / Net I/σ(I): 11.5
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.6 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.15→19.99 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 14.801 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27201 3760 5 %RANDOM
Rwork0.21921 ---
obs0.2219 70771 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.793 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.54 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7023 0 7 98 7128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0227182
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1191.9479741
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2635863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51123.51359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.146151194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3991550
X-RAY DIFFRACTIONr_chiral_restr0.1680.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025437
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.22971
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24842
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3850.2218
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1360.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2151.54352
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.227029
X-RAY DIFFRACTIONr_scbond_it3.47132830
X-RAY DIFFRACTIONr_scangle_it5.2194.52712
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 273 -
Rwork0.301 5146 -
obs--99.18 %
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)
12.3869-2.1456-0.5195.8091-0.50752.75580.0919-0.11010.4263-0.0569-0.1264-0.61560.0650.41380.03450.03560.04370.06790.35560.02740.24364.60447.76142.208
23.8512-1.5291-0.89633.41050.93522.5217-0.75890.2166-0.86140.1660.28350.42740.42340.0470.47540.42790.00950.39330.32860.00950.404565.90817.89614.244
33.5107-3.13190.06636.8624-0.14051.68290.49920.09630.7979-0.8856-0.338-1.3247-0.1895-0.0414-0.16120.24110.07860.30040.22180.10950.395447.183-5.1733.567
44.3173-1.7555-0.2313.84150.34333.8118-0.3647-0.0776-0.47690.7492-0.02940.76930.6393-0.08110.3940.53370.19360.28850.30930.00920.23217.961-1.7475.772
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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