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- PDB-1adu: EARLY E2A DNA-BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1adu
TitleEARLY E2A DNA-BINDING PROTEIN
ComponentsADENOVIRUS SINGLE-STRANDED DNA-BINDING PROTEIN
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / SSDNA BINDING PROTEIN
Function / homology
Function and homology information


viral DNA strand displacement replication / viral DNA genome replication / positive regulation of DNA replication / viral capsid / single-stranded DNA binding / DNA replication / DNA-templated transcription / host cell nucleus / DNA binding / zinc ion binding / identical protein binding
Similarity search - Function
Adenovirus Single-stranded Dna-binding Protein, domain 1 / Adenovirus DNA-binding, N-terminal domain / Adenovirus Single-stranded DNA-binding Protein; domain 2 / Adenovirus DNA-binding, C-terminal domain superfamily/Adenovirus DNA-binding, zinc binding domain / Adenovirus DNA-binding, all-alpha domain / Adenovirus DNA-binding, zinc-binding domain / Adenovirus DNA-binding, N-terminal domain superfamily / Adenovirus DNA-binding, C-terminal domain superfamily / Adenovirus DNA-binding, zinc binding domain superfamily / DNA-binding protein, Adenovirus ...Adenovirus Single-stranded Dna-binding Protein, domain 1 / Adenovirus DNA-binding, N-terminal domain / Adenovirus Single-stranded DNA-binding Protein; domain 2 / Adenovirus DNA-binding, C-terminal domain superfamily/Adenovirus DNA-binding, zinc binding domain / Adenovirus DNA-binding, all-alpha domain / Adenovirus DNA-binding, zinc-binding domain / Adenovirus DNA-binding, N-terminal domain superfamily / Adenovirus DNA-binding, C-terminal domain superfamily / Adenovirus DNA-binding, zinc binding domain superfamily / DNA-binding protein, Adenovirus / Viral DNA-binding protein, all alpha domain / Viral DNA-binding protein, zinc binding domain / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman adenovirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsTucker, P.A. / Kanellopoulos, P.N. / Tsernoglou, D. / Van Der Vliet, P.C.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Alternative arrangements of the protein chain are possible for the adenovirus single-stranded DNA binding protein.
Authors: Kanellopoulos, P.N. / Tsernoglou, D. / van der Vliet, P.C. / Tucker, P.A.
#1: Journal: Embo J. / Year: 1994
Title: Crystal Structure of the Adenovirus DNA Binding Protein Reveals a Hook-on Model for Cooperative DNA Binding
Authors: Tucker, P.A. / Tsernoglou, D. / Tucker, A.D. / Coenjaerts, F.E. / Leenders, H. / Van Der Vliet, P.C.
History
DepositionMay 11, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: 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 ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / struct_conn / struct_keywords / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _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_keywords.text / _struct_ref_seq_dif.details / _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: ADENOVIRUS SINGLE-STRANDED DNA-BINDING PROTEIN
B: ADENOVIRUS SINGLE-STRANDED DNA-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0616
Polymers79,7992
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-15 kcal/mol
Surface area28230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.000, 91.200, 149.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE MOLECULES FORM CHAINS ALONG THE CRYSTALLOGRAPHIC Z AXIS. PAIRS OF MOLECULES IN THE CHAIN ARE RELATED BY A CRYSTALLOGRAPHIC SCREW AXIS.

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Components

#1: Protein ADENOVIRUS SINGLE-STRANDED DNA-BINDING PROTEIN / ADDBP


Mass: 39899.746 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 174 - 529 / Source method: isolated from a natural source / Details: SECOND CRYSTAL FORM, DATA COLLECTED AT 293 K / Source: (natural) Human adenovirus 5 / Genus: Mastadenovirus / Cell: INFECTED HELA CELLS / Species: Human adenovirus C / References: UniProt: P03265
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 %protein1drop
213 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 27, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 17172 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.168
Reflection
*PLUS
Num. measured all: 73641
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.2 Å / Rmerge(I) obs: 0.496

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 3→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.296 -10 %
Rwork0.201 --
obs0.201 14986 86.8 %
Displacement parametersBiso mean: 35.45 Å2
Refine analyzeLuzzati coordinate error free: 0.35 Å
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 4 0 4534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.318
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_d
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 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
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_deg

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