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- PDB-1bvo: DORSAL HOMOLOGUE GAMBIF1 BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1bvo
TitleDORSAL HOMOLOGUE GAMBIF1 BOUND TO DNA
Components
  • (DNA DUPLEX) x 2
  • TRANSCRIPTION FACTOR GAMBIF1
KeywordsCOMPLEX (TRANSCRIPTION FACTOR/DNA) / TRANSCRIPTION FACTOR / REL PROTEIN / MORPHOGEN / IMMUNITY / DEVELOPMENT / INSECTS / COMPLEX (TRANSCRIPTION FACTOR-DNA) / COMPLEX (TRANSCRIPTION FACTOR-DNA) complex
Function / homology
Function and homology information


non-canonical NF-kappaB signal transduction / canonical NF-kappaB signal transduction / response to cytokine / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / innate immune response / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / cytosol
Similarity search - Function
Dorsal-related immunity factor Dif / Rel homology domain (RHD), DNA-binding domain / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain ...Dorsal-related immunity factor Dif / Rel homology domain (RHD), DNA-binding domain / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / AGAP009515-PA
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.7 Å
AuthorsCramer, P. / Varrot, A. / Barillas-Mury, C. / Kafatos, F.C. / Mueller, C.W.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Structure of the specificity domain of the Dorsal homologue Gambif1 bound to DNA.
Authors: Cramer, P. / Varrot, A. / Barillas-Mury, C. / Kafatos, F.C. / Muller, C.W.
History
DepositionSep 16, 1998Processing site: BNL
Revision 1.0Jul 12, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 11, 2017Group: Other
Revision 1.4Nov 29, 2017Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_assembly ...database_PDB_caveat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: DNA DUPLEX
E: DNA DUPLEX
A: TRANSCRIPTION FACTOR GAMBIF1


Theoretical massNumber of molelcules
Total (without water)28,8063
Polymers28,8063
Non-polymers00
Water64936
1
D: DNA DUPLEX
E: DNA DUPLEX
A: TRANSCRIPTION FACTOR GAMBIF1

D: DNA DUPLEX
E: DNA DUPLEX
A: TRANSCRIPTION FACTOR GAMBIF1


Theoretical massNumber of molelcules
Total (without water)57,6136
Polymers57,6136
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566x,-y+1,-z+3/21
Unit cell
Length a, b, c (Å)87.610, 87.610, 96.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: DNA chain DNA DUPLEX


Mass: 4584.985 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA DUPLEX


Mass: 4593.999 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein TRANSCRIPTION FACTOR GAMBIF1


Mass: 19627.447 Da / Num. of mol.: 1 / Fragment: SPECIFICITY DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Cellular location: CYTOPLASM / Plasmid: PET-15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q17034
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12-5 %PEG4001reservoir
250 mMMES1reservoir
35 mM1reservoirMgCl2
43 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.997
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 16, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 8927 / % possible obs: 82.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 93.5 Å2 / Rsym value: 0.041 / Net I/σ(I): 18.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.286 / % possible all: 88.5
Reflection
*PLUS
Num. measured all: 33776 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 88.5 % / Rmerge(I) obs: 0.286

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR / Resolution: 2.7→10 Å / Rfactor Rfree error: 0.014 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: AT EARLY STAGES, PROGRAM REFMAC WAS USED. TO ACCOUNT FOR AVERAGED BASE PAIRS (D6-D10, E26-E30), TWO STRUCTURES CONTAINING DIFFERENT DNA STRANDS (CHAIN E AND D) WERE REFINED INDIVIDUALLY. AT ...Details: AT EARLY STAGES, PROGRAM REFMAC WAS USED. TO ACCOUNT FOR AVERAGED BASE PAIRS (D6-D10, E26-E30), TWO STRUCTURES CONTAINING DIFFERENT DNA STRANDS (CHAIN E AND D) WERE REFINED INDIVIDUALLY. AT A FINAL STAGE, BOTH DNA STRANDS WERE INCLUDED IN THE MODEL AND GIVEN HALF OCCUPANCY. CYS 126 AND CYS 131 ARE IN CLOSE PROXIMITY AND THE ELECTRON DENSITY WOULD ALSO ALLOW MODELING OF A DISULPHIDE BRIDGE. THIS MIGHT INDICATE PARTIAL OXIDATION. LOOP 81-84 IS BADLY ORDERED. DURING REFINEMENT, IT HAS BEEN GIVEN AN OCCUPANCY OF 0.5. LYS 222 IS THE LAST RESIDUE IN THE MODEL. THE QUALITY OF ITS ELECTRON DENSITY IS POOR AND DID NOT ALLOW UNAMBIGUOUS MODELING. THE C-TERMINAL DIMERIZATION DOMAIN OF THE REL HOMOLOGY REGION OF GAMBIF1 IS PRESENT IN THE USED CONSTRUCT AND THE CRYSTALS. HOWEVER, IT IS DISORDERED AND COULD NOT BE INCLUDED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 404 4.7 %RANDOM
Rwork0.219 ---
obs0.219 8575 84.1 %-
Displacement parametersBiso mean: 52.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.84 Å2--
2---3.84 Å2-
3---7.68 Å2
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1377 609 0 36 2022
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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_it3.62.5
X-RAY DIFFRACTIONx_mcangle_it5.62.5
X-RAY DIFFRACTIONx_scbond_it6.43.5
X-RAY DIFFRACTIONx_scangle_it8.73.5
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.426 51 5 %
Rwork0.436 1013 -
obs--88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA.PARAMTOPH19.PEP
X-RAY DIFFRACTION3PARAM19.SOLDNA-RNA.TOP
X-RAY DIFFRACTION4TOPH19.SOL

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