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- PDB-1cmv: HUMAN CYTOMEGALOVIRUS PROTEASE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1cmv
TitleHUMAN CYTOMEGALOVIRUS PROTEASE
ComponentsHUMAN CYTOMEGALOVIRUS PROTEASE
KeywordsSERINE PROTEASE / COAT PROTEIN / HYDROLASE / PHOSPHORYLATION
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
Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 5
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.27 Å
AuthorsShieh, H.-S. / Kurumbail, R.G. / Stevens, A.M. / Stegeman, R.A. / Sturman, E.J. / Pak, J.Y. / Wittwer, A.J. / Palmier, M.O. / Wiegand, R.C. / Holwerda, B.C. / Stallings, W.C.
Citation
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Activity of Two-Chain Recombinant Human Cytomegalovirus Protease
Authors: Holwerda, B.C. / Wittwer, A.J. / Duffin, K.L. / Smith, C. / Toth, M.V. / Carr, L.S. / Wiegand, R.C. / Bryant, M.L.
History
DepositionAug 26, 1996Processing site: BNL
Revision 1.0Sep 4, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN CYTOMEGALOVIRUS PROTEASE
B: HUMAN CYTOMEGALOVIRUS PROTEASE


Theoretical massNumber of molelcules
Total (without water)56,1432
Polymers56,1432
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-23 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.800, 76.800, 172.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.392218, -0.271165, 0.878996), (-0.263403, -0.948658, -0.175122), (0.881354, -0.162844, -0.443506)-7.2715, 194.6194, 70.2344
2given(0.405727, -0.27594, 0.871345), (-0.279633, -0.9451, -0.169091), (0.870167, -0.175052, -0.460615)-6.6904, 194.38, 73.104
3given(0.396748, -0.268844, 0.877675), (-0.266262, -0.948746, -0.170252), (0.878462, -0.166144, -0.447996)-7.4793, 194.3765, 71.1344
4given(0.398005, -0.270915, 0.876469), (-0.277369, -0.946222, -0.166522), (0.874447, -0.176829, -0.451745)-7.295, 194.2774, 72.6372
5given(0.398051, -0.269216, 0.876971), (-0.26717, -0.94855, -0.169922), (0.877597, -0.166663, -0.449497)-7.5779, 194.4319, 71.2938

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Components

#1: Protein HUMAN CYTOMEGALOVIRUS PROTEASE / HCMV PROTEASE


Mass: 28071.480 Da / Num. of mol.: 2 / Mutation: V141A, A144P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 / Genus: Cytomegalovirus / Plasmid: PMON9059 / Production host: Escherichia coli (E. coli)
References: UniProt: P16753, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.5
Details: 28-30% MONOMETHYL POLYETHYLENE GLYCOL 550 0.05-0.2 M NACL 10% GLYCEROL 50 MM HEPES AT PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
128-33 %mPEG5501reservoir
20.05-0.2 M1reservoirNaCl
310 %glycerol1reservoir
450 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 24, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.27→40 Å / Num. obs: 23705 / % possible obs: 94.5 % / Observed criterion σ(I): -1.5 / Redundancy: 12.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.38
Reflection shellResolution: 2.26→2.34 Å / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 1.81 / % possible all: 75.7
Reflection
*PLUS
Num. measured all: 297289
Reflection shell
*PLUS
% possible obs: 75.7 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.27→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.31 -10 %
Rwork0.241 --
obs0.241 19433 -
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 2.27→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 0 18 3173
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.311
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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