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- PDB-4ekf: Structure of the Inactive Adenovirus Proteinase at 0.98 Angstrom ... -

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Basic information

Entry
Database: PDB / ID: 4ekf
TitleStructure of the Inactive Adenovirus Proteinase at 0.98 Angstrom Resolution
ComponentsAdenain
KeywordsHYDROLASE / alpha and beta protein (a+b)
Function / homology
Function and homology information


adenain / cysteine-type peptidase activity / virion component / cysteine-type endopeptidase activity / host cell nucleus / proteolysis / DNA binding
Similarity search - Function
Peptidase C5, adenain / Adenovirus endoprotease / Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman adenovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.98 Å
AuthorsBaniecki, M.L. / McGrath, W.J. / Mangel, W.F.
Citation
Journal: J.Biol.Chem. / Year: 2013
Title: Regulation of a Viral Proteinase by a Peptide and DNA in One-dimensional Space: III. ATOMIC RESOLUTION STRUCTURE OF THE NASCENT FORM OF THE ADENOVIRUS PROTEINASE.
Authors: Baniecki, M.L. / McGrath, W.J. / Mangel, W.F.
#1: Journal: J.Biol.Chem. / Year: 2012
Title: Regulation of a viral proteinase by a peptide and DNA in one-dimensional space. I. binding to DNA and to hexon of the precursor to protein VI, pVI, of human adenovirus.
Authors: Graziano, V. / McGrath, W.J. / Suomalainen, M. / Greber, U.F. / Freimuth, P. / Blainey, P.C. / Luo, G. / Xie, X.S. / Mangel, W.F.
#2: Journal: J.Biol.Chem. / Year: 2012
Title: Regulation of a viral proteinase by a peptide and DNA in one-dimensional space. II. adenovirus proteinase is activated in an unusual one-dimensional biochemical reaction.
Authors: Graziano, V. / Luo, G. / Blainey, P.C. / Perez-Berna, A.J. / McGrath, W.J. / Flint, S.J. / San Martin, C. / Xie, X.S. / Mangel, W.F.
#3: Journal: J.Biol.Chem. / Year: 2012
Title: Regulation of a viral proteinase by a peptide and DNA in one-dimensional space. IV. viral proteinase slides along DNA to locate and process its substrates.
Authors: Blainey, P.C. / Graziano, V. / Perez-Berna, A.J. / McGrath, W.J. / Flint, S.J. / San Martin, C. / Xie, X.S. / Mangel, W.F.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Adenovirus proteinase: crystallization and preliminary X-ray diffraction studies to atomic resolution.
Authors: Baniecki, M.L. / McGrath, W.J. / Dauter, Z. / Mangel, W.F.
#5: 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.
#6: 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.
#7: 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 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Database references
Revision 1.3Feb 6, 2013Group: Database references
Revision 1.4Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.5Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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Assembly

Deposited unit
A: Adenain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1692
Polymers23,1461
Non-polymers231
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.270, 54.540, 42.410
Angle α, β, γ (deg.)90.00, 100.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23146.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 2 / Strain: serotype 2 / Gene: L3-23K / Plasmid: pET 13a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLys S / References: UniProt: P03252, adenain
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.75 Å3/Da / Density % sol: 29.2 %
Crystal growTemperature: 293 K / pH: 5.6
Details: 0.3M sodium citrate, pH 5.6, 0.8 M sodium acetate, 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.92
DetectorType: BRANDEIS 4K / Detector: CCD / Date: Jul 28, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 0.98→30 Å / Num. obs: 92231 / % possible obs: 99.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 8.59 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 25.4
Reflection shellResolution: 0.98→1 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.594 / % possible all: 97.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NLN CHAIN A

1nln


Resolution: 0.98→20 Å / Num. parameters: 16135 / Num. restraintsaints: 19747 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1678 --RANDOM
all0.135 90549 --
obs0.135 92231 97.3 %-
Displacement parametersBiso mean: 17.7814 Å2
Refine analyzeLuzzati coordinate error obs: 0.127 Å / Num. disordered residues: 12 / Occupancy sum hydrogen: 1406 / Occupancy sum non hydrogen: 1732.98
Refinement stepCycle: LAST / Resolution: 0.98→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 1 258 1794
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.029
X-RAY DIFFRACTIONs_angle_d0.045
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0278
X-RAY DIFFRACTIONs_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.172
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.119
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.079

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