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- PDB-6ey7: Human cytomegalovirus terminase nuclease domain, Mn soaked, inhib... -

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Basic information

Entry
Database: PDB / ID: 6ey7
TitleHuman cytomegalovirus terminase nuclease domain, Mn soaked, inhibitor bound
ComponentsUL89 HCMV terminase
KeywordsVIRAL PROTEIN / Cytomegalovirus / UL89 / terminase / inhibitors / drug design / raltegravir
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
Chem-C3W / : / Tripartite terminase subunit 3
Similarity search - Component
Biological speciesHuman herpesvirus 5 strain AD169
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBongarzone, S. / Nadal, M. / Kaczmarska, Z. / Machon, C. / Alvarez, M. / Albericio, F. / Coll, M.
Funding support Spain, Belgium, 5items
OrganizationGrant numberCountry
Ministry of Economy and CompetitivenessBFU2011-22588 Spain
Ministry of Economy and CompetitivenessCTQ2012-30930 Spain
Ministry of Economy and CompetitivenessCTQ2015-67870P Spain
Ministry of Economy and CompetitivenessBFU2014-53550-P Spain
European UnionSILVER-GA 260644 Belgium
CitationJournal: Acs Omega / Year: 2018
Title: Structure-Driven Discovery of alpha , gamma-Diketoacid Inhibitors Against UL89 Herpesvirus Terminase.
Authors: Bongarzone, S. / Nadal, M. / Kaczmarska, Z. / Machon, C. / Alvarez, M. / Albericio, F. / Coll, M.
History
DepositionNov 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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.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.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UL89 HCMV terminase
B: UL89 HCMV terminase
C: UL89 HCMV terminase
D: UL89 HCMV terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,86919
Polymers127,2724
Non-polymers1,59815
Water45025
1
A: UL89 HCMV terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2365
Polymers31,8181
Non-polymers4184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UL89 HCMV terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1814
Polymers31,8181
Non-polymers3633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UL89 HCMV terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2365
Polymers31,8181
Non-polymers4184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UL89 HCMV terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2165
Polymers31,8181
Non-polymers3994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.650, 87.650, 186.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
UL89 HCMV terminase


Mass: 31817.889 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 strain AD169 / Gene: UL89 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16732
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-C3W / 4-[(4-fluorophenyl)methyl-methyl-amino]-2,4-bis(oxidanylidene)butanoic acid


Mass: 253.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H12FNO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% Mes 1M pH 6.5, 6% PEG8000 and 150 mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9194, 1.240
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91941
21.241
ReflectionResolution: 2.9→30 Å / Num. obs: 30097 / % possible obs: 98.8 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rrim(I) all: 0.08 / Net I/σ(I): 14.4
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1502 / CC1/2: 0.654 / Rrim(I) all: 1.03 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N4P

3n4p


Resolution: 2.9→29.87 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.869 / Cross valid method: THROUGHOUT / σ(F): 1.34 / SU R Blow DPI: 0.794 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.276
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1503 5 %RANDOM
Rwork0.175 ---
obs0.176 30080 98.9 %-
Displacement parametersBiso mean: 89.34 Å2
Baniso -1Baniso -2Baniso -3
1--2.478 Å20 Å20 Å2
2--5.9244 Å20 Å2
3----3.4464 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.9→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6810 0 83 25 6918
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017029HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.099561HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2291SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1239HARMONIC5
X-RAY DIFFRACTIONt_it7029HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion19.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion974SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7654SEMIHARMONIC4
LS refinement shellResolution: 2.9→3 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2472 138 4.7 %
Rwork0.2385 2799 -
all0.2389 2937 -
obs--99.73 %
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)
13.659-1.18430.05896.2325-0.06383.29890.1215-0.3527-0.32450.51490.02570.0740.1071-0.4257-0.1472-0.2107-0.0299-0.0482-0.13320.0111-0.1369-24.2289-46.554243.4683
24.7821-1.50220.86215.1483-0.72772.8342-0.27680.03510.4592-0.0484-0.0027-0.4129-0.1302-0.18280.2795-0.24750.03230.0057-0.2373-0.08080.0138-25.8557-17.081115.0653
34.7222-1.994-0.2044.8651.04292.3468-0.172-0.2413-0.31870.44580.01140.35170.00570.10240.1606-0.18620.0306-0.0521-0.29380.02750.0698-6.82645.926433.5686
45.5196-2.1086-0.07214.1777-0.24553.81370.04450.07670.545-0.32980.1039-0.4367-0.25720.1728-0.1484-0.2313-0.0418-0.0767-0.2597-0.03850.028821.47712.06035.1506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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