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- PDB-5v5e: Room temperature (280K) crystal structure of Kaposi's sarcoma-ass... -

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Basic information

Entry
Database: PDB / ID: 5v5e
TitleRoom temperature (280K) crystal structure of Kaposi's sarcoma-associated herpesvirus protease in complex with allosteric inhibitor (compound 733)
ComponentsORF 17
KeywordsVIRAL PROTEIN / INHIBITOR / protease / allosteric inhibitor / herpesvirus / VIRAL PROTEIN - 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-8N4 / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.299 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)43,9275
Polymers42,3862
Non-polymers1,5413
Water77543
1
A: 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
2
B: 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
3
A: ORF 17
hetero molecules

B: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9275
Polymers42,3862
Non-polymers1,5413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_444x-1/2,-y-1/2,-z-1/21
Buried area1880 Å2
ΔGint-13 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.400, 96.840, 119.080
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-324-

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-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.: 43 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Imidazole pH 8.0 0.34M sodium phosphate monobasic 1.36M potassium phosphate dibasic 0.2M potassium chloride

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.3→31.156 Å / Num. obs: 18827 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.684 % / Biso Wilson estimate: 43.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.123 / Χ2: 0.891 / Net I/σ(I): 9.31 / Num. measured all: 69361 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.363.7480.9561.714978139813280.551.11695
2.36-2.423.7160.8042.044965136613360.620.93797.8
2.42-2.493.6430.7092.174762134413070.7060.83297.2
2.49-2.573.5540.6242.624482128812610.7330.73497.9
2.57-2.653.3380.5662.794005127412000.7680.67594.2
2.65-2.753.7390.473.654464121211940.8520.5598.5
2.75-2.853.6920.3884.434297118111640.8990.45598.6
2.85-2.973.710.3165.514081111811000.9120.3798.4
2.97-3.13.6990.2477.164010109410840.9520.28899.1
3.1-3.253.7610.1689.873908104610390.9750.19599.3
3.25-3.433.5150.1311.66337810009610.9810.15296.1
3.43-3.633.9040.09914.3136359429310.9910.11398.8
3.63-3.883.9280.08815.6834928948890.9930.10199.4
3.88-4.23.8670.06918.4532028348280.9940.07999.3
4.2-4.63.7960.05421.9728817707590.9950.06298.6
4.6-5.143.4420.0521.3523067016700.9960.05895.6
5.14-5.933.9220.05421.6924166216160.9960.06299.2
5.93-7.273.7740.05222.0219745355230.9960.06197.8
7.27-10.283.3420.04126.2513574324060.9960.04994
10.28-31.1563.3250.03829.887682592310.9970.04489.2

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3njq


Resolution: 2.299→31.156 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 919 4.89 %
Rwork0.1986 17890 -
obs0.2002 18809 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 224.79 Å2 / Biso mean: 66.2831 Å2 / Biso min: 22.92 Å2
Refinement stepCycle: final / Resolution: 2.299→31.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 186 43 3082
Biso mean--57.93 41.58 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023113
X-RAY DIFFRACTIONf_angle_d0.6254273
X-RAY DIFFRACTIONf_chiral_restr0.044485
X-RAY DIFFRACTIONf_plane_restr0.004540
X-RAY DIFFRACTIONf_dihedral_angle_d16.2111847
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 (%)
2.2988-2.41990.3361150.31172521263697
2.4199-2.57150.31761300.29612503263398
2.5715-2.76990.32851420.30412478262097
2.7699-3.04840.3071330.27122575270899
3.0484-3.4890.24821260.19552552267898
3.489-4.39380.2061400.15752611275199
4.3938-31.15840.16441330.1522650278397
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)
10.594-0.05781.07030.8098-0.55311.8664-0.21240.03940.07130.16690.0396-0.1314-0.33940.114-0.10830.30780.01-0.07850.2926-0.01330.3547-21.1458-9.7664-36.43
20.6755-0.35190.17280.37470.1450.3375-0.31060.12480.44890.09750.00990.0465-0.6353-0.0872-0.0030.56130.0136-0.12840.45780.02270.4828-19.2625-5.0132-33.0777
30.7305-0.2707-0.55170.56210.21840.9437-0.35010.26020.01630.03820.53360.1325-0.31370.5006-0.15660.5185-0.1079-0.2680.56320.08140.5433-9.7305-8.7519-35.9745
40.1536-0.15470.34820.4709-0.58510.7311-0.12780.32470.160.24810.152-0.0303-0.45040.01930.00230.4351-0.0436-0.06310.3796-0.03180.3782-6.7274-17.9394-6.2476
51.19210.54280.57951.52930.18020.2807-0.09150.03690.2061-0.24360.0776-0.2122-0.6354-0.2188-0.04960.42370.1351-0.09060.35530.01360.3395-11.4791-15.981-9.1549
61.07430.45460.33170.6563-0.45440.9006-0.04060.0243-0.1015-0.15670.08810.1709-0.074-0.122500.29290.021-0.05170.2623-0.01650.2686-9.9314-28.0971-10.5685
70.1447-0.0386-0.0150.1209-0.05350.0188-0.2217-0.1394-0.09210.17530.04060.0891-0.1437-0.059-0.00190.38570.0386-0.09360.3120.02220.3415-7.8375-19.0595-5.7768
80.3768-0.07010.10220.464-0.1260.29980.1915-0.08430.0976-0.00580.1220.15880.3761-0.58970.00320.3025-0.0073-0.02610.6040.03820.4226-24.0709-29.2596-4.1316
90.0254-0.0502-0.05841.3129-0.28550.25040.2046-0.1744-0.0917-0.6402-0.3114-0.0381-0.3468-0.00520.08340.45870.1038-0.12660.56750.05090.2868-13.5907-25.846-23.3177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 122 )A4 - 122
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 160 )A123 - 160
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 193 )A161 - 193
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 22 )B4 - 22
5X-RAY DIFFRACTION5chain 'B' and (resid 23 through 52 )B23 - 52
6X-RAY DIFFRACTION6chain 'B' and (resid 53 through 122 )B53 - 122
7X-RAY DIFFRACTION7chain 'B' and (resid 123 through 148 )B123 - 148
8X-RAY DIFFRACTION8chain 'B' and (resid 149 through 177 )B149 - 177
9X-RAY DIFFRACTION9chain 'B' and (resid 178 through 195 )B178 - 195

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