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- PDB-4p55: Crystal structure of DNA binding domain of K11 from KSHV -

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Basic information

Entry
Database: PDB / ID: 4p55
TitleCrystal structure of DNA binding domain of K11 from KSHV
ComponentsViral IRF2-like protein
KeywordsDNA BINDING PROTEIN / interferon regulatory factor
Function / homology
Function and homology information


symbiont-mediated suppression of host PKR/eIFalpha signaling / transcription cis-regulatory region binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus
Similarity search - Function
IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Viral IRF2-like protein
Similarity search - Component
Biological speciesHuman herpesvirus 8 type P
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.504 Å
AuthorsHu, H.D. / Gao, Z.Q. / Lan, K. / Dong, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)10979005 and 31200552 China
CitationJournal: To Be Published
Title: crystal structure of DNA binding domain of K11 from KSHV
Authors: Hu, H.D. / Gao, Z.Q. / Lan, K. / Dong, Y.H.
History
DepositionMar 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_symm_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Viral IRF2-like protein
B: Viral IRF2-like protein


Theoretical massNumber of molelcules
Total (without water)26,1912
Polymers26,1912
Non-polymers00
Water1,53185
1
A: Viral IRF2-like protein


Theoretical massNumber of molelcules
Total (without water)13,0951
Polymers13,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Viral IRF2-like protein


Theoretical massNumber of molelcules
Total (without water)13,0951
Polymers13,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.467, 48.467, 195.088
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Viral IRF2-like protein / vIRF-2


Mass: 13095.466 Da / Num. of mol.: 2 / Fragment: UNP residues 7-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 type P / Strain: isolate GK18 / Gene: vIRF-2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2HR71
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.04 M Citric acid, 0.1 M BIS-TRIS propane (pH 6.8), 17% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 5, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 9881 / % possible obs: 100 % / Redundancy: 15.3 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 29.55
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 3.95 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.504→41.035 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 472 4.8 %Random selection
Rwork0.2104 ---
obs0.2123 9827 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.504→41.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1699 0 0 85 1784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011744
X-RAY DIFFRACTIONf_angle_d1.2572344
X-RAY DIFFRACTIONf_dihedral_angle_d15.64660
X-RAY DIFFRACTIONf_chiral_restr0.081231
X-RAY DIFFRACTIONf_plane_restr0.005305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.504-2.86640.32941540.24633042X-RAY DIFFRACTION100
2.8664-3.61110.29131510.22873050X-RAY DIFFRACTION100
3.6111-41.04010.20761670.193263X-RAY DIFFRACTION100

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