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- PDB-3njq: Crystal structure of Kaposi's sarcoma-associated herpesvirus prot... -

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Basic information

Entry
Database: PDB / ID: 3njq
TitleCrystal structure of Kaposi's sarcoma-associated herpesvirus protease in complex with dimer disruptor
Components(ORF 17) x 2
KeywordsVIRAL PROTEIN/INHIBITOR / protein-dimer disruptor complex / KSHV / KSHV protease / herpesvirus protease / 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
ACETATE ION / Chem-NJQ / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 8 type M
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBaharuddin, A.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Enzyme inhibition by allosteric capture of an inactive conformation.
Authors: Lee, G.M. / Shahian, T. / Baharuddin, A. / Gable, J.E. / Craik, C.S.
History
DepositionJun 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)44,15910
Polymers42,4342
Non-polymers1,7258
Water1,928107
1
B: ORF 17
hetero molecules

A: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,15910
Polymers42,4342
Non-polymers1,7258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544x+1/2,-y-1/2,-z-1/21
Buried area2850 Å2
ΔGint-39 kcal/mol
Surface area18460 Å2
MethodPISA
2
A: ORF 17
B: ORF 17
hetero molecules

A: ORF 17
B: ORF 17
hetero molecules

A: ORF 17
B: ORF 17
hetero molecules

A: ORF 17
B: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,63640
Polymers169,7378
Non-polymers6,90032
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area16240 Å2
ΔGint-191 kcal/mol
Surface area69710 Å2
MethodPISA
3
B: ORF 17
hetero molecules

B: ORF 17
hetero molecules

B: ORF 17
hetero molecules

B: ORF 17
hetero molecules

A: ORF 17
hetero molecules

A: ORF 17
hetero molecules

A: ORF 17
hetero molecules

A: ORF 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,63640
Polymers169,7378
Non-polymers6,90032
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation5_545x+1/2,y-1/2,z+1/21
crystal symmetry operation6_445-x-1/2,-y-1/2,z+1/21
crystal symmetry operation7_444-x-1/2,y-1/2,-z-1/21
crystal symmetry operation8_544x+1/2,-y-1/2,-z-1/21
Buried area26170 Å2
ΔGint-278 kcal/mol
Surface area59780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.317, 95.994, 119.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ORF 17


Mass: 21209.111 Da / Num. of mol.: 1 / Fragment: UNP residues 23-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 type M / Gene: Rhadinovirus / Plasmid: pet16b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)pLysS / References: UniProt: P88911
#2: Protein ORF 17


Mass: 21225.111 Da / Num. of mol.: 1 / Fragment: UNP residues 23-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 type M / Gene: Rhadinovirus / Plasmid: pet16b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)pLysS / References: UniProt: P88911

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Non-polymers , 5 types, 115 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NJQ / 3-benzyl-4-({[6-(cyclohexylmethyl)pyridin-2-yl]carbonyl}amino)benzoic acid


Mass: 428.523 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H28N2O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: 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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Details

Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M NaCl, 0.05M CaCo, 2M (NH4)2SO4, 0.1M Urea, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 210 / Detector: CCD / Date: Feb 15, 2010 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 27034 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.044.10.581100
2.04-2.084.10.4981100
2.08-2.134.10.431100
2.13-2.184.10.3851100
2.18-2.244.10.3111100
2.24-2.314.10.2781100
2.31-2.384.10.2431100
2.38-2.474.10.2021100
2.47-2.574.10.1731100
2.57-2.684.10.1541100
2.68-2.824.10.124199.9
2.82-34.10.1199.9
3-3.234.10.071199.9
3.23-3.5640.0471100
3.56-4.073.90.033199.5
4.07-5.134.10.0251100
5.13-5040.019199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å47.99 Å
Translation2.5 Å47.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 9.858 / SU ML: 0.138 / Stereochemistry target values: Engh & Huber / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflection
Rfree0.248 1366 5 %
Rwork0.203 --
obs0.205 25855 99.9 %
all-27246 -
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.272 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refine analyzeLuzzati coordinate error free: 0.176 Å
Refinement stepCycle: LAST / Resolution: 2→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 121 107 3165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213171
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9792.0144343
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.95.153391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.99623.167120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80715470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4071518
X-RAY DIFFRACTIONr_chiral_restr0.1490.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0222391
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9261.51918
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57523135
X-RAY DIFFRACTIONr_scbond_it2.4431253
X-RAY DIFFRACTIONr_scangle_it3.5394.51203
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å
RfactorNum. reflection% reflection
Rfree0.325 101 -
Rwork0.27 1870 -
obs--99.95 %
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)
11.52360.16811.79052.04940.66738.0391-0.2368-0.0090.15920.24220.0851-0.2558-0.90220.48980.15170.1574-0.0395-0.08140.08620.02450.1893-17.6742-8.8851-35.5835
22.5984-0.781-0.43863.10630.31373.7643-0.06410.01260.0932-0.01520.0030.1101-0.32-0.32860.06110.03960.0326-0.0290.04680.00390.0749-12.1955-24.0641-9.4674
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 193
2X-RAY DIFFRACTION2B4 - 195

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