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

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Basic information

Entry
Database: PDB / ID: 5uvp
TitleKaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric Inhibitor
ComponentsORF 17
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Serine Hydrolase / Viral Protein / Capsid Maturation / HYDROLASE-HYDROLASE 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-8N7 / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 20, 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)43,7745
Polymers42,3862
Non-polymers1,3883
Water3,729207
1
A: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1183
Polymers21,1931
Non-polymers9252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6562
Polymers21,1931
Non-polymers4631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.604, 92.573, 119.152
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
11B-363-

HOH

21B-367-

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-8N7 / 6-(cyclohexylmethyl)-N-{2-[(oxan-4-yl)oxy]-4-(1H-tetrazol-5-yl)phenyl}pyridine-2-carboxamide


Mass: 462.544 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H30N6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Sodium acetate pH 5.5, 0.8M NaH2PO4/1.2M K2HPO4

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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: 1.94→73.103 Å / Num. obs: 27625 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.174 / Net I/σ(I): 6.6

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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: 1.94→73.103 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2163 1998 7.25 %
Rwork0.1944 25561 -
obs0.196 27559 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.68 Å2 / Biso mean: 43.2159 Å2 / Biso min: 18.35 Å2
Refinement stepCycle: final / Resolution: 1.94→73.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2815 0 189 207 3211
Biso mean--62.72 39.18 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073044
X-RAY DIFFRACTIONf_angle_d0.9744198
X-RAY DIFFRACTIONf_chiral_restr0.052493
X-RAY DIFFRACTIONf_plane_restr0.006531
X-RAY DIFFRACTIONf_dihedral_angle_d14.0351820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-1.98860.33571430.28721823196699
1.9886-2.04230.30661380.26051782192099
2.0423-2.10240.28811410.25961792193399
2.1024-2.17030.28681410.24051805194699
2.1703-2.24790.25591400.22981785192599
2.2479-2.33790.26051420.221118141956100
2.3379-2.44430.28621410.218118151956100
2.4443-2.57310.26251420.209218211963100
2.5731-2.73440.21821420.209818131955100
2.7344-2.94550.22321430.19818231966100
2.9455-3.24190.16851410.1891819196099
3.2419-3.7110.16751460.167118471993100
3.711-4.67540.18541450.155118662011100
4.6754-73.15470.211530.184919562109100

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