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- PDB-1o6e: Epstein-Barr virus protease -

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Basic information

Entry
Database: PDB / ID: 1o6e
TitleEpstein-Barr virus protease
ComponentsCAPSID PROTEIN P40
KeywordsHYDROLASE / PROTEINASE / BETA-BARREL / SERINE PROTEASE / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS
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
PHOSPHORYLISOPROPANE / Capsid scaffolding protein
Similarity search - Component
Biological speciesHUMAN HERPESVIRUS 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBuisson, M. / Hernandez, J. / Lascoux, D. / Schoehn, G. / Forest, E. / Arlaud, G. / Seigneurin, J. / Ruigrok, R.W.H. / Burmeister, W.P.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The Crystal Structure of the Epstein-Barr Virus Protease Shows Rearrangement of the Processed C Terminus
Authors: Buisson, M. / Hernandez, J. / Lascoux, D. / Schoehn, G. / Forest, E. / Arlaud, G. / Seigneurin, J. / Ruigrok, R.W.H. / Burmeister, W.P.
History
DepositionSep 13, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2002Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAPSID PROTEIN P40
B: CAPSID PROTEIN P40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1284
Polymers50,8482
Non-polymers2802
Water21612
1
A: CAPSID PROTEIN P40
B: CAPSID PROTEIN P40
hetero molecules

A: CAPSID PROTEIN P40
B: CAPSID PROTEIN P40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2568
Polymers101,6964
Non-polymers5604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area8520 Å2
ΔGint-52.8 kcal/mol
Surface area41340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.800, 52.800, 330.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9993, 0.0239, 0.0285), (0.0355, 0.845, 0.5336), (-0.0113, 0.5342, -0.8453)
Vector: 7.3, -13.89, 47.02)

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Components

#1: Protein CAPSID PROTEIN P40 / ASSEMBLIN / VIRION STRUCTURAL PROTEIN BVRF2 / EC-RF3 AND EC-RF3A / PROTEASE / CAPSID PROTEIN VP22A


Mass: 25423.990 Da / Num. of mol.: 2
Fragment: COAT PROTEIN VP24 (PROTEASE) DOMAIN, RESIDUES 1-235
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus)
Strain: B95-8 / Cell line: B95-8 MARMOSET CELL LINE / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03234, assemblin
#2: Chemical ChemComp-ISP / PHOSPHORYLISOPROPANE


Mass: 140.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9O4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION ARG 64 SER, CHAINS A AND B
Has protein modificationY
Sequence detailsONLY PROTEASE DOMAIN OF THE ASSEMBLIN IS PRESENT IN THE CRYSTAL.THE SEQUENCE IS MODIFIED AT THE N- ...ONLY PROTEASE DOMAIN OF THE ASSEMBLIN IS PRESENT IN THE CRYSTAL.THE SEQUENCE IS MODIFIED AT THE N-TERMINUS DUE TO THE INTRODUCTION OF A THROMBIN CLEAVAGE SITE.

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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: 2.57 Å3/Da / Density % sol: 52 % / Description: CRYSTAL TWINNED
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: HANGING DROP METHOD USING A RESERVOIR SOLUTION OF 1.25 - 1.5 M SODIUM FORMATE,100 MM SODIUM CITRATE PH4.6 5 MM EDTA, PROTEIN IN 100 MM NACL 20 MM THRIS-HCL PH 7.5 1 MM EDTA 10 MM BETA-MERCAPTOETHANOL
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115-21 mg/mlprotein1drop
2100 mM1dropNaCl
3200 mMTris-HCl1droppH7.5
41 mMEDTA1drop
510 mMbeta-mercaptoethanol1drop
610 mMDFP1drop
71.25-1.5 Msodium formate1reservoir
8100 mMsodium citrate1reservoiror acetate, pH4.6
95 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.919
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2001 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.3→45.2 Å / Num. obs: 132854 / % possible obs: 98.1 % / Redundancy: 5.4 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 5.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.3 / % possible all: 89.9
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 89.9 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FL1

1fl1


Resolution: 2.3→42 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINED USING THE TWINNED TARGET, TWINNING FRACTION 0.477, OPERATOR -H,-K,L THE REFINEMENT HAS BEEN CARRIED OUT AGAINST TWINNED DATA USING THE CORRESPONDING TARGET IN CNS. R-FACTORS CAN NOT ...Details: REFINED USING THE TWINNED TARGET, TWINNING FRACTION 0.477, OPERATOR -H,-K,L THE REFINEMENT HAS BEEN CARRIED OUT AGAINST TWINNED DATA USING THE CORRESPONDING TARGET IN CNS. R-FACTORS CAN NOT DIRECTLY BE COMPARED TO THE ONES FROM UNTWINNED STRUCTURES. FOR MAP CALCULATIONS, A DIFFERENT DATASET WITH A TWINNING FRACTION MORE DIFFERENT FROM 0.5 HAS BEEN USED. ITS RESOLUTION WAS LIMITED TO 2.5 A. SOME REGIONS CARACTERISED BY B FACTORS ABOVE 90 A2 ARE POORLY DEFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1149 5 %RANDOM
Rwork0.197 ---
obs0.197 24212 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.6 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso mean: 66.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.95 Å2-7.3 Å20 Å2
2---8.95 Å20 Å2
3---17.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-42 Å
Luzzati sigma a0.64 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 2.3→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3483 0 14 12 3509
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.932.5
X-RAY DIFFRACTIONc_mcangle_it5.023
X-RAY DIFFRACTIONc_scbond_it34
X-RAY DIFFRACTIONc_scangle_it4.774
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.382 91 5 %
Rwork0.386 1813 -
obs--89.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM.DFPTOPH3.DFP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2

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