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- PDB-5ur3: Kaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric ... -

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Basic information

Entry
Database: PDB / ID: 5ur3
TitleKaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric Inhibitor
ComponentsKSHV protease
KeywordsHYDROLASE/HYDROLASE inhibitor / Serine Hydrolase / Viral Protein / Capsid Maturation / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


assemblin / 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-8OY / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAcker, T.M. / Gable, J. / Bohn, M.-F. / Craik, C.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH R01 GM104659 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F32GM111012 United States
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 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KSHV protease
B: KSHV protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6755
Polymers42,3862
Non-polymers1,2893
Water4,035224
1
A: KSHV protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6232
Polymers21,1931
Non-polymers4301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KSHV protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0523
Polymers21,1931
Non-polymers8592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.400, 92.860, 118.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-363-

HOH

21B-403-

HOH

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Components

#1: Protein KSHV protease / ORF17 / ORF 17


Mass: 21193.111 Da / Num. of mol.: 2 / Fragment: UNP 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-8OY / 4-{[6-(cyclohexylmethyl)pyridine-2-carbonyl]amino}-3-(phenylamino)benzoic acid


Mass: 429.511 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H27N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 43.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.3M 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
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→59.47 Å / Num. obs: 37258 / % possible obs: 99.8 % / Redundancy: 7.2 % / Net I/σ(I): 21.4

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Processing

Software
NameVersionClassification
PHENIX1.10PRE_2100refinement
xia2data reduction
SCALAdata scaling
PHENIXPhenix 1.8.4 Phaser 2.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→58.64 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1761 5.05 %
Rwork0.18 --
obs0.182 34879 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.43 Å2
Refinement stepCycle: LAST / Resolution: 1.8→58.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2921 0 96 224 3241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143196
X-RAY DIFFRACTIONf_angle_d1.3394394
X-RAY DIFFRACTIONf_dihedral_angle_d17.1551883
X-RAY DIFFRACTIONf_chiral_restr0.076501
X-RAY DIFFRACTIONf_plane_restr0.01568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84870.2871250.24012500X-RAY DIFFRACTION100
1.8487-1.90310.25821510.22382480X-RAY DIFFRACTION99
1.9031-1.96450.24351230.2062543X-RAY DIFFRACTION100
1.9645-2.03470.24391320.19682510X-RAY DIFFRACTION100
2.0347-2.11620.22041380.18232526X-RAY DIFFRACTION100
2.1162-2.21250.22721540.17832496X-RAY DIFFRACTION100
2.2125-2.32920.26161110.18112548X-RAY DIFFRACTION100
2.3292-2.47510.24761390.18682533X-RAY DIFFRACTION100
2.4751-2.66620.25051290.18512568X-RAY DIFFRACTION100
2.6662-2.93450.24521420.1882559X-RAY DIFFRACTION100
2.9345-3.35910.20191460.17562538X-RAY DIFFRACTION100
3.3591-4.2320.181240.15472613X-RAY DIFFRACTION100
4.232-58.66930.21061470.17322704X-RAY DIFFRACTION100

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