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- PDB-1nln: CRYSTAL STRUCTURE OF HUMAN ADENOVIRUS 2 PROTEINASE WITH ITS 11 AM... -

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Basic information

Entry
Database: PDB / ID: 1nln
TitleCRYSTAL STRUCTURE OF HUMAN ADENOVIRUS 2 PROTEINASE WITH ITS 11 AMINO ACID COFACTOR AT 1.6 ANGSTROM RESOLUTION
Components
  • Adenain
  • PVIC
KeywordsHYDROLASE / THIOL HYDROLASE / VIRAL PROTEINASE / PEPTIDE COFACTOR
Function / homology
Function and homology information


nuclear capsid assembly / adenain / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / cysteine-type peptidase activity / virion component / host cell / viral capsid ...nuclear capsid assembly / adenain / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / cysteine-type peptidase activity / virion component / host cell / viral capsid / host cell cytoplasm / cysteine-type endopeptidase activity / host cell nucleus / proteolysis / DNA binding
Similarity search - Function
Peptidase C5, adenain / Adenovirus endoprotease / Minor capsid protein VI / Minor capsid protein VI / Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Protease / Pre-protein VI
Similarity search - Component
Biological speciesHuman adenovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMcGrath, W.J. / Ding, J. / Sweet, R.M. / Mangel, W.F.
Citation
Journal: Biochim.Biophys.Acta / Year: 2003
Title: Crystallographic structure at 1.6-A resolution of the human adenovirus proteinase in a covalent complex with its 11-amino-acid peptide cofactor: insights on a new fold
Authors: McGrath, W.J. / Ding, J. / Didwania, A. / Sweet, R.M. / Mangel, W.F.
#1: Journal: Embo J. / Year: 1996
Title: Crystal Structure of the Human Adenovirus Proteinase with its 11 Amino-acid Cofactor
Authors: Ding, J. / McGrath, W.J. / Sweet, R.M. / Mangel, W.F.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: Characterization of Three Components of Human Adenovirus Proteinase Activity in vitro
#3: Journal: Nature / Year: 1993
Title: Viral DNA and a Viral Peptide can act as Cofactors of Adenovirus Virion Proteinase Activity
History
DepositionJan 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Adenain
B: PVIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5283
Polymers24,4682
Non-polymers601
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-4 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.500, 111.500, 50.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Adenain / Endoprotease / Late L3 23 kDa protein


Mass: 23114.350 Da / Num. of mol.: 1 / Fragment: adenovirus proteinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 2 / Genus: Mastadenovirus / Species: Human adenovirus C / Gene: L3-23k / Plasmid: pET13 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03252, adenain
#2: Protein/peptide PVIC


Mass: 1353.640 Da / Num. of mol.: 1 / Fragment: pvic peptide / Source method: obtained synthetically
Details: chemically synthesized C-terminal 11 amino acids from human adenovirus serotype 2 pVI molecule
References: UniProt: P03274*PLUS
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: cacodylate, sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: McGrath, W.J., (1996) J. Struct. Biol., 117, 77.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Aug 10, 1995 / Details: collimator
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 44449 / % possible obs: 92.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 30.6
Reflection shellResolution: 1.6→50 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 7.7 / Num. unique all: 3674 / Rsym value: 0.154 / % possible all: 77.1
Reflection
*PLUS
Num. obs: 44447 / Num. measured all: 166648
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.66 Å / % possible obs: 77.1 % / Mean I/σ(I) obs: 7.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1AVP

1avp


Resolution: 1.6→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.179 4380 -random
Rwork0.136 ---
obs-44447 92.5 %-
Displacement parametersBiso mean: 14.1 Å2
Refine analyze
FreeObs
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 0 242 1957
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_mcangle_it2.1
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_mcangle_it
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.66 Å

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