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- PDB-5ute: Kaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric ... -

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Basic information

Entry
Database: PDB / ID: 5ute
TitleKaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric Inhibitor
ComponentsORF 17
KeywordsVIRAL PROTEIN/INHIBITOR / Serine Hydrolase / Viral Protein / Capsid Maturation / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


assemblin / nuclear capsid assembly / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / proteolysis / identical protein binding
Similarity search - Function
Serine Protease, Human Cytomegalovirus Protease; Chain A / Herpesvirus/Caudovirus protease domain / Peptidase S21 / Herpesvirus protease superfamily / Assemblin (Peptidase family S21) / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-8M4 / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsAcker, T.M. / Gable, J. / Bohn, M.-F. / Craik, C.S.
CitationJournal: To Be Published
Title: Kaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric Inhibitor
Authors: Acker, T.M. / Craik, C.S. / Bohn, M.-F.
History
DepositionFeb 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: ORF 17
B: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7655
Polymers42,3862
Non-polymers1,3793
Water6,503361
1
A: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1123
Polymers21,1931
Non-polymers9192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6532
Polymers21,1931
Non-polymers4601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.330, 93.328, 119.147
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-319-

HOH

31A-351-

HOH

41A-407-

HOH

51B-393-

HOH

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Components

#1: Protein ORF 17 / ORF17


Mass: 21193.111 Da / Num. of mol.: 2 / Fragment: residues 23-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF17 / Production host: Escherichia coli (E. coli) / References: UniProt: O40922
#2: Chemical ChemComp-8M4 / 4-{[6-(cyclohexylmethyl)pyridine-2-carbonyl]amino}-3-[(4-methoxyphenyl)amino]benzoic acid


Mass: 459.537 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H29N3O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 0.2M Imidazole pH 8.0, 0.4M NaH2PO4/1.6M K2HPO4, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→73.47 Å / Num. obs: 46042 / % possible obs: 100 % / Redundancy: 15.4 % / Rmerge(I) obs: 0.374 / Net I/σ(I): 8.97

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Processing

Software
NameVersionClassification
PHENIX1.10pre_2100refinement
PDB_EXTRACT3.22data extraction
SCALA3.3.21data scaling
PHENIXPhenix 1.8.4 Phaser 2.1phasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NJQ

3njq


Resolution: 2.05→73.472 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.45 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 2438 5.3 %
Rwork0.1828 43604 -
obs0.1855 24222 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.83 Å2 / Biso mean: 23.6024 Å2 / Biso min: 7.61 Å2
Refinement stepCycle: final / Resolution: 2.05→73.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2827 0 146 361 3334
Biso mean--20.4 31.31 -
Num. residues----375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143017
X-RAY DIFFRACTIONf_angle_d1.4474141
X-RAY DIFFRACTIONf_chiral_restr0.082479
X-RAY DIFFRACTIONf_plane_restr0.009525
X-RAY DIFFRACTIONf_dihedral_angle_d14.0941751
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.09190.35961240.26082541266598
2.0919-2.13730.29451410.23322589273098
2.1373-2.18710.26681590.22222526268599
2.1871-2.24180.31011860.23582504269099
2.2418-2.30240.33141470.24822528267599
2.3024-2.37010.30331720.214525552727100
2.3701-2.44660.29491310.203225932724100
2.4466-2.53410.29021420.196925412683100
2.5341-2.63560.28471230.194625852708100
2.6356-2.75550.25861300.197626302760100
2.7555-2.90080.2681400.194425492689100
2.9008-3.08250.24611350.171925912726100
3.0825-3.32050.18231550.161325552710100
3.3205-3.65470.1791190.151525762695100
3.6547-4.18350.19351290.139625872716100
4.1835-5.27060.15761530.140925822735100
5.2706-73.51890.22341520.201625722724100

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