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- PDB-1jq7: HCMV protease dimer-interface mutant, S225Y complexed to Inhibito... -

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Basic information

Entry
Database: PDB / ID: 1jq7
TitleHCMV protease dimer-interface mutant, S225Y complexed to Inhibitor BILC 408
ComponentsASSEMBLIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Herpesvirus / cytomegalovirus / serine protease / dimerization / enzyme activity regulation / HYDROLASE-HYDROLASE 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
N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~4~,N~4~-dimethyl-N~1~-[(1R)-1-methyl-2,3-dioxo-3-{[(1S)-1- phenylpropyl]amino}propyl]-L-aspartamide / Chem-0FP / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBatra, R. / Khayat, R. / Tong, L.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Molecular mechanism for dimerization to regulate the catalytic activity of human cytomegalovirus protease.
Authors: Batra, R. / Khayat, R. / Tong, L.
History
DepositionAug 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details
Revision 1.7Nov 20, 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: ASSEMBLIN
B: ASSEMBLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8494
Polymers56,4132
Non-polymers1,4362
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-18 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.250, 74.250, 215.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ASSEMBLIN / PROTEASE


Mass: 28206.641 Da / Num. of mol.: 2 / Mutation: A143Q, S225Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 / Production host: Escherichia coli (E. coli) / References: UniProt: P16753, assemblin
#2: Chemical ChemComp-0FP / N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~1~-[(2S,3S)-3-hydroxy-4-oxo-4-{[(1R)-1-phenylpropyl]amino}butan-2-yl]-N~4~,N~4~-dimethyl-L-aspartamide / BILC 408


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 717.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H63N7O7 / Details: This peptide was chemically synthesized.
References: N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~4~,N~4~-dimethyl-N~1~-[(1R)-1-methyl-2,3-dioxo-3-{[(1S)-1- phenylpropyl]amino}propyl]-L-aspartamide
Has protein modificationY
Nonpolymer detailsTHE INHIBITOR 0FP IS COVALENTLY CONNECTED AT CARBON C4 TO THE ACTIVE SITE SERINES (A 1132 AND B ...THE INHIBITOR 0FP IS COVALENTLY CONNECTED AT CARBON C4 TO THE ACTIVE SITE SERINES (A 1132 AND B 1432) VIA HEMIKETAL LINKAGES

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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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, HEPES, sodium chloride, glycerol, spermine tetrahydrochloride, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / Details: Tong, L., (1998) Nature Struct. Biol., 5, 819.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 mg/mlprotein1drop
218 %PEG40001reservoir
30.1 MHEPES1reservoirpH7.5
40.2 M1reservoirNaCl
510 %glycerol1reservoir
650 mMspermine1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 2, 2001
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3→19.9 Å / Num. all: 48246 / Num. obs: 10900 / % possible obs: 85.5 % / Observed criterion σ(F): 7 / Observed criterion σ(I): 5
Reflection shellResolution: 3→3.19 Å / % possible all: 97
Reflection
*PLUS
Num. measured all: 48246 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Rmerge(I) obs: 0.129

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Processing

Software
NameVersionClassification
COMOphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WPO (dimer)

2wpo


Resolution: 3→19.99 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2061042.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 7 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.339 809 7.4 %RANDOM
Rwork0.26 ---
all0.28 48246 --
obs-10900 85.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.250918 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1-10.71 Å20 Å20 Å2
2--10.71 Å20 Å2
3----21.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.41 Å
Luzzati d res low-7 Å
Luzzati sigma a-0.11 Å
Refinement stepCycle: LAST / Resolution: 3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 86 0 3395
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it0.921.5
X-RAY DIFFRACTIONc_mcangle_it1.562
X-RAY DIFFRACTIONc_scbond_it1.152
X-RAY DIFFRACTIONc_scangle_it1.732.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 96 7.5 %
Rwork0.281 1185 -
obs-1200 62.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2C408.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 7 / % reflection Rfree: 7.4 % / Rfactor obs: 0.26 / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.36 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.281

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