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- PDB-5v5d: Room temperature (280K) crystal structure of Kaposi's sarcoma-ass... -

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Basic information

Entry
Database: PDB / ID: 5v5d
TitleRoom temperature (280K) crystal structure of Kaposi's sarcoma-associated herpesvirus protease in complex with allosteric inhibitor (compound 250)
ComponentsORF 17
KeywordsVIRAL PROTEIN / INHIBITOR / protease / allosteric inhibitor / herpesvirus / 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-8OY / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.104 Å
AuthorsThompson, M.C. / Acker, T.M. / Fraser, J.S. / Craik, C.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI090592 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F32GM111012 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5F32HL129989-03 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases.
Authors: Acker, T.M. / Gable, J.E. / Bohn, M.F. / Jaishankar, P. / Thompson, M.C. / Fraser, J.S. / Renslo, A.R. / Craik, C.S.
History
DepositionMar 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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

Downloads & links

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Assembly

Deposited unit
A: ORF 17
B: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6755
Polymers42,3862
Non-polymers1,2893
Water1,928107
1
A: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6232
Polymers21,1931
Non-polymers4301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0523
Polymers21,1931
Non-polymers8592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.060, 94.090, 119.680
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-353-

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-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.: 107 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1M Sodium acetate pH 7.8 0.88M Sodium Phosphate monobasic 1.32M Potassium phosphate dibasic 0.2M potassium chloride

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2015
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.1→47.045 Å / Num. obs: 20562 / % possible obs: 89.3 % / Observed criterion σ(I): -3 / Redundancy: 4.636 % / Biso Wilson estimate: 28.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.115 / Χ2: 1.079 / Net I/σ(I): 13.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.164.5180.792.4415310.7840.88391.8
2.16-2.224.5090.5973.315110.8670.66892
2.22-2.284.5630.5653.6914450.8810.63292.1
2.28-2.354.5580.4684.414370.9150.52392.4
2.35-2.434.5740.4554.9113790.9110.50991.8
2.43-2.524.60.3826.113160.9340.42890.7
2.52-2.614.6740.3327.112990.9490.37191.1
2.61-2.724.6810.2568.7712130.9670.28790.3
2.72-2.844.6660.21910.4711610.9640.24589.7
2.84-2.984.7020.16313.3311190.9820.18289.2
2.98-3.144.6950.1216.5310640.9890.13488.5
3.14-3.334.7090.09320.099920.9930.10488.5
3.33-3.564.6830.06824.559190.9960.07687.6
3.56-3.844.7010.05727.178700.9980.06486.5
3.84-4.214.7170.0530.967940.9970.05587.2
4.21-4.714.6230.03835.577000.9990.04284.1
4.71-5.434.7960.03436.66260.9980.03884.3
5.43-6.654.8370.03734.55290.9990.04183.2
6.65-9.414.760.03139.184200.9990.03482.4
9.41-47.0454.4560.02642.562370.9990.02977.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXdev_2686refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NJQ

3njq


Resolution: 2.104→47.045 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.33
RfactorNum. reflection% reflection
Rfree0.2106 1024 4.98 %
Rwork0.1744 --
obs0.1762 20558 89.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 179.21 Å2 / Biso mean: 41.4725 Å2 / Biso min: 7.65 Å2
Refinement stepCycle: final / Resolution: 2.104→47.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2923 0 171 107 3201
Biso mean--30.13 32.43 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033214
X-RAY DIFFRACTIONf_angle_d0.5954413
X-RAY DIFFRACTIONf_chiral_restr0.045506
X-RAY DIFFRACTIONf_plane_restr0.003566
X-RAY DIFFRACTIONf_dihedral_angle_d16.8461887
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1042-2.21510.2691640.2412792295692
2.2151-2.35390.26261350.21952863299892
2.3539-2.53570.25731500.20842846299691
2.5357-2.79080.23731570.19732774293190
2.7908-3.19460.2291490.1842755290489
3.1946-4.02450.20261410.15272767290887
4.0245-47.05670.15811280.14232737286583
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)
10.2179-0.2625-0.05070.28110.07890.28650.0467-0.0115-0.03630.1981-0.1742-0.08890.01590.1699-0.02910.2279-0.0744-0.03430.320.10610.29-8.0223-42.5819-28.7665
20.862-0.1888-0.23770.0953-0.01741.1680.0312-0.0645-0.1263-0.04310.02530.0270.0171-0.172400.2275-0.02680.01120.23590.01740.2358-15.422-36.6869-38.7714
3-0.007-0.0332-0.01650.06940.06120.0815-0.1492-0.329-0.02680.0774-0.0866-0.0836-0.20350.3924-0.00050.2462-0.0107-0.01220.45580.07040.2283-9.2802-42.8862-23.1608
40.5661-0.3416-0.02090.28940.07280.0198-0.1252-0.1128-0.22020.10210.0317-0.00420.10720.17120.00010.3269-0.01290.03040.3670.03180.32-11.1732-42.4233-27.7824
50.51330.05040.3050.16460.10680.3560.05850.1369-0.1846-0.0114-0.04230.08230.127-0.54030.06560.1829-0.07260.00430.3399-0.00410.3466-26.3328-46.033-38.9489
60.53060.25410.24530.2059-0.0211.2150.00590.1248-0.0103-0.2534-0.14790.0995-0.4807-0.0834-0.21450.23930.060.1140.3324-0.08530.3514-20.76-25.4151-34.3656
70.2282-0.0927-0.42110.2620.4670.6038-0.1572-0.0166-0.16630.1740.012-0.07290.21060.0119-0.01460.2770.00540.05170.22140.01930.2421-27.4866-30.6879-4.4834
80.7430.0486-0.19050.84130.37460.9353-0.01060.09570.0136-0.1141-0.0072-0.04320.20970.2081-0.00260.22780.03740.03980.1743-0.00830.1869-20.4288-24.927-11.1754
90.2538-0.2062-0.090.2174-0.04080.19080.29110.08260.42720.12130.0427-0.5189-0.17930.24140.00370.31680.00960.00620.2476-0.02690.3994-30.3954-4.3674-8.9263
100.3395-0.20810.29710.0666-0.12830.24630.021-0.09220.08990.0601-0.14310.26220.0210.083700.19410.01410.00820.16550.01170.1922-26.1211-16.0626-7.84
110.2317-0.2787-0.06030.14710.01910.1449-0.1668-0.1312-0.0677-0.03870.07270.05080.25910.0614-0.00710.3380.02640.05970.19010.01390.2557-26.8037-31.7318-5.393
120.1491-0.0829-0.05860.36320.13690.06630.0521-0.13970.1783-0.02950.0888-0.0071-0.24370.56020.00860.2174-0.07190.02570.3378-0.04250.2092-13.6224-15.3256-2.6728
130.1698-0.06790.1660.6530.13330.3316-0.1632-0.09080.07350.18330.3092-0.5730.05970.2310.00390.24610.04760.01810.5699-0.04950.383-5.841-23.3222-8.1334
140.0583-0.1053-0.01530.13070.0540.14210.06460.26970.16170.0198-0.13330.03630.13220.136700.34540.05610.04760.3246-0.04620.2537-26.0555-21.0524-24.7658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 26 )A4 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 109 )A27 - 109
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 124 )A110 - 124
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 148 )A125 - 148
5X-RAY DIFFRACTION5chain 'A' and (resid 149 through 177 )A149 - 177
6X-RAY DIFFRACTION6chain 'A' and (resid 178 through 194 )A178 - 194
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 26 )B4 - 26
8X-RAY DIFFRACTION8chain 'B' and (resid 27 through 86 )B27 - 86
9X-RAY DIFFRACTION9chain 'B' and (resid 87 through 100 )B87 - 100
10X-RAY DIFFRACTION10chain 'B' and (resid 101 through 116 )B101 - 116
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 148 )B117 - 148
12X-RAY DIFFRACTION12chain 'B' and (resid 149 through 165 )B149 - 165
13X-RAY DIFFRACTION13chain 'B' and (resid 166 through 183 )B166 - 183
14X-RAY DIFFRACTION14chain 'B' and (resid 184 through 196 )B184 - 196

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