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- PDB-5uv3: Kaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric ... -

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Basic information

Entry
Database: PDB / ID: 5uv3
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-8N4 / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 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)43,9275
Polymers42,3862
Non-polymers1,5413
Water4,342241
1
A: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2203
Polymers21,1931
Non-polymers1,0272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7072
Polymers21,1931
Non-polymers5141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.326, 95.828, 118.997
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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-8N4 / 4-{[6-(cyclohexylmethyl)pyridine-2-carbonyl]amino}-3-{[3-(trifluoromethoxy)phenyl]amino}benzoic acid


Mass: 513.508 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H26F3N3O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Imidazole pH 8.0, 0.42M NaH2PO4/1.68M K2HPO4, 0.2M KCl

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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: 1.95→61.2 Å / Num. obs: 57222 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.243 / Net I/σ(I): 10.93

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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: 1.95→61.178 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.45 / Phase error: 27.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2366 2914 5.09 %
Rwork0.2016 54308 -
obs0.2034 30117 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.65 Å2 / Biso mean: 36.7903 Å2 / Biso min: 13.86 Å2
Refinement stepCycle: final / Resolution: 1.95→61.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2813 0 111 241 3165
Biso mean--30.85 40.23 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163016
X-RAY DIFFRACTIONf_angle_d1.7924154
X-RAY DIFFRACTIONf_chiral_restr0.098481
X-RAY DIFFRACTIONf_plane_restr0.012527
X-RAY DIFFRACTIONf_dihedral_angle_d18.0431057
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.9820.34541370.30012548268598
1.982-2.01620.32611180.27212572269098
2.0162-2.05290.34021570.2592570272799
2.0529-2.09230.3311600.25452527268799
2.0923-2.13510.2771480.23612561270999
2.1351-2.18150.3041120.244226022714100
2.1815-2.23220.30111190.23782625274499
2.2322-2.28810.31541460.226325702716100
2.2881-2.34990.24041220.228926282750100
2.3499-2.41910.2531080.208125942702100
2.4191-2.49720.26621580.210825662724100
2.4972-2.58640.25351590.212525782737100
2.5864-2.690.25081620.218625742736100
2.69-2.81240.28871490.213826132762100
2.8124-2.96070.31191320.207225772709100
2.9607-3.14610.2311210.208526152736100
3.1461-3.3890.235950.193426582753100
3.389-3.73010.19251400.173125822722100
3.7301-4.26970.18231480.159325822730100
4.2697-5.37890.16431430.156825952738100
5.3789-61.20820.21061800.202425712751100

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