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- PDB-1at3: HERPES SIMPLEX VIRUS TYPE II PROTEASE -

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Basic information

Entry
Database: PDB / ID: 1at3
TitleHERPES SIMPLEX VIRUS TYPE II PROTEASE
ComponentsHERPES SIMPLEX VIRUS TYPE II PROTEASE
KeywordsSERINE PROTEASE / VIRAL PROTEASE / HSV2 PROTEASE
Function / homology
Function and homology information


assemblin / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / 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
DIISOPROPYL PHOSPHONATE / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 2
MethodX-RAY DIFFRACTION / molecular replacement, MIR / Resolution: 2.5 Å
AuthorsHoog, S. / Smith, W.W. / Qiu, X. / Abdel-Meguid, S.S.
CitationJournal: Biochemistry / Year: 1997
Title: Active site cavity of herpesvirus proteases revealed by the crystal structure of herpes simplex virus protease/inhibitor complex.
Authors: Hoog, S.S. / Smith, W.W. / Qiu, X. / Janson, C.A. / Hellmig, B. / McQueney, M.S. / O'Donnell, K. / O'Shannessy, D. / DiLella, A.G. / Debouck, C. / Abdel-Meguid, S.S.
History
DepositionAug 16, 1997Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_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.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_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: HERPES SIMPLEX VIRUS TYPE II PROTEASE
B: HERPES SIMPLEX VIRUS TYPE II PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4444
Polymers54,1122
Non-polymers3322
Water77543
1
A: HERPES SIMPLEX VIRUS TYPE II PROTEASE
B: HERPES SIMPLEX VIRUS TYPE II PROTEASE
hetero molecules

A: HERPES SIMPLEX VIRUS TYPE II PROTEASE
B: HERPES SIMPLEX VIRUS TYPE II PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8898
Polymers108,2244
Non-polymers6654
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-11 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.720, 87.430, 77.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper: (Code: given
Matrix: (0.931609, 0.05004, 0.36), (0.06423, -0.997555, -0.027556), (0.357741, 0.048794, -0.932545)
Vector: -8.0172, 46.2017, 34.6584)

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Components

#1: Protein HERPES SIMPLEX VIRUS TYPE II PROTEASE


Mass: 27055.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DIISOPROPYL PHOSPHATE COVALENTLY BOUND TO ACTIVE SITE SER 129
Source: (gene. exp.) Human herpesvirus 2 / Genus: Simplexvirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q69527
#2: Chemical ChemComp-DFP / DIISOPROPYL PHOSPHONATE


Mass: 166.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O3P
#3: Water ChemComp-HOH / water / 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: 2.57 Å3/Da / Density % sol: 52 %
Crystal growpH: 5 / Details: 10% PEG4000, PH 5.0
Crystal
*PLUS
Density % sol: 45 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %PEG40001reservoirpH5.0
210 mg/mlenzyme1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 78502 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 12
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3 / Rsym value: 0.24 / % possible all: 88
Reflection
*PLUS
Num. obs: 15788 / Num. measured all: 78502

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
XDSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: molecular replacement, MIR
Starting model: 1VZV

1vzv


Resolution: 2.5→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1475 10.1 %RANDOM
Rwork0.205 ---
obs0.205 14605 85.6 %-
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 20 43 3356
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.49
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.111.5
X-RAY DIFFRACTIONx_mcangle_it4.92
X-RAY DIFFRACTIONx_scbond_it4.792
X-RAY DIFFRACTIONx_scangle_it7.342.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNCS model detailsRms dev position (Å)Weight Biso Weight positionRms dev Biso (Å2)
11RESTRAINED0.227250
2200
3300
4400
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.268 124 10.4 %
Rwork0.228 1064 -
obs--57.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PAHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
X-RAY DIFFRACTION4
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.49

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