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- PDB-1avp: STRUCTURE OF HUMAN ADENOVIRUS 2 PROTEINASE WITH ITS 11 AMINO ACID... -

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Basic information

Entry
Database: PDB / ID: 1avp
TitleSTRUCTURE OF HUMAN ADENOVIRUS 2 PROTEINASE WITH ITS 11 AMINO ACID COFACTOR
Components(ADENOVIRAL PROTEINASEAdenoviridae) x 2
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 / viral capsid / host cell cytoplasm ...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 / 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
Protease / Pre-protein VI
Similarity search - Component
Biological speciesHuman adenovirus 2
Human adenovirus C
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS SOFTWARE USED : NULL STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL / Resolution: 2.6 Å
AuthorsDing, J. / Mcgrath, W.J. / Sweet, R.M. / Mangel, W.F.
Citation
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.
#1: Journal: To be Published
Title: Characterization of the Human Adenovirus Proteinase Activity in Disrupted Virus Particles
Authors: Mcgrath, W.J. / Abola, A.P. / Toledo, D.L. / Brown, M.T. / Mangel, W.F.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: Characterization of Three Components of Human Adenovirus Activity in Vitro
Authors: Mangel, W.F. / Toledo, D.L. / Brown, M.T. / Martin, J.H. / Mcgrath, W.J.
#3: Journal: Nature / Year: 1993
Title: Viral DNA and a Viral Peptide Can Act as Cofactors of Adenovirus Virion Proteinase Activity
Authors: Mangel, W.F. / Mcgrath, W.J. / Toledo, D.L. / Anderson, C.W.
History
DepositionApr 4, 1996Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 25, 2016Group: Structure summary
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Remark 700SHEET SHEET SHEET_ID: (), DETERMINATION METHOD: PROCHECK.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADENOVIRAL PROTEINASE
B: ADENOVIRAL PROTEINASE


Theoretical massNumber of molelcules
Total (without water)24,4682
Polymers24,4682
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-7 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.300, 114.300, 50.000
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 ADENOVIRAL PROTEINASE / Adenoviridae / AVP


Mass: 23114.350 Da / Num. of mol.: 1 / Fragment: MAIN
Source method: isolated from a genetically manipulated source
Details: PVIC PEPTIDE COFACTOR DISULFIDE BONDS TO CYS104 OF AVP
Source: (gene. exp.) Human adenovirus 2 / Genus: Mastadenovirus / Species: Human adenovirus C / Fragment: MAIN / Plasmid: PET 13 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P03252
#2: Protein/peptide ADENOVIRAL PROTEINASE / Adenoviridae / PVIC


Mass: 1353.640 Da / Num. of mol.: 1 / Fragment: PEPT / Source method: obtained synthetically
Details: PVIC PEPTIDE IS CHEMICALLY SYNTHESIZED PVIC PEPTIDE COFACTOR DISULFIDE BONDS TO CYS104 OF AVP
Source: (synth.) Human adenovirus C / References: UniProt: P03274
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 4

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.06 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Density % sol: 68 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: McGrath, W.J., (1996) J. Struct. Biol., 117, 77. / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMHEPES1reservoirpH7.5
21.4-1.6 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 10, 1995 / Details: COLLIMATOR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 11559 / % possible obs: 98.8 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 20
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 16 / % possible all: 97.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement
RefinementMethod to determine structure: SIRAS SOFTWARE USED : NULL STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL
Resolution: 2.6→6 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1086 10 %RANDOM
Rwork0.184 ---
obs0.184 11559 98.8 %-
Refine analyzeLuzzati coordinate error obs: 0.1 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 0 45 1760
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.169
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
LS refinement shellResolution: 2.6→2.64 Å / Rfactor Rfree error: 0.053 /
RfactorNum. reflection
Rfree0.334 39
Rwork0.216 420
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PRO,TOPH19.PEPTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.169

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