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- PDB-1anv: ADENOVIRUS 5 DBP/URANYL FLUORIDE SOAK -

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Basic information

Entry
Database: PDB / ID: 1anv
TitleADENOVIRUS 5 DBP/URANYL FLUORIDE SOAK
ComponentsADENOVIRUS SINGLE-STRANDED DNA-BINDING PROTEIN
KeywordsDNA BINDING PROTEIN / EARLY PROTEIN / DNA-BINDING PROTEIN / ZINC-FINGER / PHOSPHORYLATION / NUCLEAR 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
URANYL (VI) ION / DNA-binding protein
Similarity search - Component
Biological speciesHuman adenovirus 5
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKanellopoulos, P.N. / Tsernoglou, D. / Van Der Vliet, P.C. / Tucker, P.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Conformational change of the adenovirus DNA-binding protein induced by soaking crystals with K3UO2F5 solutions.
Authors: Kanellopoulos, P.N. / Tsernoglou, D. / van der Vliet, P.C. / Tucker, P.A.
#1: 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.
#2: 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
DepositionMar 14, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Structure summary / Category: diffrn_source / struct_keywords / Item: _diffrn_source.type / _struct_keywords.text
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADENOVIRUS SINGLE-STRANDED DNA-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1117
Polymers39,9001
Non-polymers1,2116
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.700, 75.600, 60.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 39899.746 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 174 - 529 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 5 / Genus: Mastadenovirus / Species: Human adenovirus C / References: UniProt: P03265
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2U
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growpH: 5.8 / Details: pH 5.8
Crystal grow
*PLUS
Method: vapor diffusion / Details: Tsernoglou, D., (1984) J. Mol. Biol., 172, 237.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 %protein1drop
213 %satammonium sulfate1drop

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 27, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→15 Å / Num. obs: 10312 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.147
Reflection shellResolution: 2.7→3.2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.342 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 34497

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Processing

Software
NameClassification
AMoREphasing
TNTrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ADT

1adt
PDB Unreleased entry


Resolution: 2.7→15 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.31 -10 %
Rwork0.204 --
obs-10312 98.7 %
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 6 31 2500
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.71
X-RAY DIFFRACTIONt_dihedral_angle_d26.8
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.206 / Rfactor Rfree: 0.314
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg26.8

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