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- PDB-2wb0: 2.1 resolution structure of the C-terminal domain of the human ad... -

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Basic information

Entry
Database: PDB / ID: 2wb0
Title2.1 resolution structure of the C-terminal domain of the human adenovirus 5 ssDNA binding protein
ComponentsE2A 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
DNA-binding protein / DNA-binding protein
Similarity search - Component
Biological speciesHUMAN ADENOVIRUS 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHendle, J. / Kanellopoulos, P.N. / Tucker, P.A.
CitationJournal: To be Published
Title: High Resolution Structures of the Adenovirus Single-Stranded DNA Binding Protein and the N512P Hinge-Region Mutant
Authors: Hendle, J. / Kanellopoulos, P.N. / Tucker, P.A.
History
DepositionFeb 19, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionMar 31, 2010ID: 1ADT
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_atom_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: E2A DNA-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0313
Polymers39,9001
Non-polymers1312
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.290, 76.660, 64.690
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 E2A DNA-BINDING PROTEIN / ADENOVIRUS 5 SSDNA BINDING PROTEIN


Mass: 39899.746 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DNA BINDING DOMAIN, RESIDUES 174-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN ADENOVIRUS 5 / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q2KS06, UniProt: P03265*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.42 Å3/Da / Density % sol: 48.83 % / Description: NONE
Crystal growpH: 5.8 / Details: pH 5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.928
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 1.95→15 Å / Num. obs: 29937 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.3
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ADT

1adt
PDB Unreleased entry


Resolution: 1.95→14.95 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.258 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 299 TO 327 AND 456 TO 463 COULD NOT BE MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1436 5 %RANDOM
Rwork0.184 ---
obs0.187 27042 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.45 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2471 0 2 383 2856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222555
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.251.9433459
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2215313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18324.359117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.68115426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7441511
X-RAY DIFFRACTIONr_chiral_restr0.2820.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211941
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3551.51581
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.32322541
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5773974
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5364.5918
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 101 -
Rwork0.218 1946 -
obs--99.51 %

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