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- PDB-1fl1: KSHV PROTEASE -

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Basic information

Entry
Database: PDB / ID: 1fl1
TitleKSHV PROTEASE
ComponentsPROTEASE
KeywordsVIRAL PROTEIN / serine protease / antiviral drug design / capsid maturation / endopeptidase / assemblin
Function / homology
Function and homology information


viral process / host cell cytoplasm / serine-type endopeptidase activity / proteolysis
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
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsReiling, K.K. / Pray, T.R. / Craik, C.S. / Stroud, R.M.
Citation
Journal: Biochemistry / Year: 2000
Title: Functional consequences of the Kaposi's sarcoma-associated herpesvirus protease structure: regulation of activity and dimerization by conserved structural elements.
Authors: Reiling, K.K. / Pray, T.R. / Craik, C.S. / Stroud, R.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallography & NMR System: A new software suite for macromolecular structure determination
Authors: Brunger, A.T. / Adams, P.D. / Clore, G.M. / Delano, W.L. / Gros, P. / Grosse-Kunstleve, R. / Jiang, J.-S. / Kuszewski, J. / Nilges, M. / Pannu, N.S. / Read, R.J. / Rice, L.M. / Simonson, T. / Warren, G.
History
DepositionAug 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEASE
B: PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4993
Polymers50,4602
Non-polymers391
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-25 kcal/mol
Surface area17250 Å2
MethodPISA
2
A: PROTEASE
B: PROTEASE
hetero molecules

A: PROTEASE
B: PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,9986
Polymers100,9204
Non-polymers782
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area6750 Å2
ΔGint-57 kcal/mol
Surface area33150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.58, 53.58, 323.06
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number152
Space group name H-MP3121
DetailsThe biological active enzyme is a homo-dimer constructed from chain A and B related by a Non-crystalographic two-fold.

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Components

#1: Protein PROTEASE


Mass: 25229.938 Da / Num. of mol.: 2 / Mutation: S204G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Genus: Rhadinovirus / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: O36607
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG-2K, 100 mM Tris-HCl, 10% glycerol, 190 mM LiSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 25K
Crystal
*PLUS
Density % sol: 53.7 %
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 mg/mlprotein1drop
20.2 mMt-Boc-YLKA-chloromethyl ketone1drop
32.0 %acetate1drop
410 mMpotassium phosphate1drop
54 %glycerol1drop
60.4 mMdithiothreitol1drop
78.8 %PEG20001drop
840 mMTris-HCl1drop
94 %glycerol1drop
1076 mM1dropLiSO4
1122 %PEG20001reservoir
12100 mMTris-HCl1reservoir
1310 %glycerol1reservoir
14190 mM1reservoirLiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 3, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→28.282 Å / Num. all: 28220 / Num. obs: 28034 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 41.658 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.2
Reflection shellResolution: 2.2→2.22 Å / Redundancy: 5 % / Rmerge(I) obs: 0.351 / Num. unique all: 905 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
CNS1refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementResolution: 2.2→28 Å / σ(F): 0 / σ(I): 0
Stereochemistry target values: Cambridge Data Base model structures (R. A. Engh and R. Huber, Acta Cryst. Sect. A., 1991).
Details: RESIDUES 182 AND 207 HAD DENSITY ONLY TO THE CG AND WERE MODELED AS SERINES DURING REFINEMENT.
RfactorNum. reflectionSelection details
Rfree0.2597 1642 RANDOM
Rwork0.2253 --
all0.2253 27951 -
obs0.2253 27951 -
Refinement stepCycle: LAST / Resolution: 2.2→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2987 0 1 195 3183
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.561
X-RAY DIFFRACTIONx_angle_deg3.8
X-RAY DIFFRACTIONx_torsion_deg24.2
X-RAY DIFFRACTIONx_torsion_impr_deg2.79
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 28 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg3.8

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