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- PDB-1fjl: HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLI... -

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Basic information

Entry
Database: PDB / ID: 1fjl
TitleHOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLIGONUCLEOTIDE
Components
  • DNA (5'-D(*AP*AP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*AP*GP*AP*TP*TP*AP*T)-3')
  • DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3')
  • PAIRED PROTEIN
KeywordsTRANSCRIPTION/DNA / DNA-BINDING PROTEIN / DNA / PAIRED BOX / TRANSCRIPTION REGULATION / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


periodic partitioning by pair rule gene / HATs acetylate histones / anatomical structure development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Paired domain / Paired DNA-binding domain / PAX family / 'Paired box' domain / Paired DNA-binding domain signature. / Paired DNA-binding domain profile. / Paired Box domain / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain ...Paired domain / Paired DNA-binding domain / PAX family / 'Paired box' domain / Paired DNA-binding domain signature. / Paired DNA-binding domain profile. / Paired Box domain / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Segmentation protein paired
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWilson, D.S. / Guenther, B. / Desplan, C. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1995
Title: High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA.
Authors: Wilson, D.S. / Guenther, B. / Desplan, C. / Kuriyan, J.
History
DepositionDec 17, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 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: PAIRED PROTEIN
B: PAIRED PROTEIN
C: PAIRED PROTEIN
D: DNA (5'-D(*AP*AP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3')
E: DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*AP*GP*AP*TP*TP*AP*T)-3')
F: DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)41,9776
Polymers41,9776
Non-polymers00
Water4,378243
1
A: PAIRED PROTEIN
B: PAIRED PROTEIN
D: DNA (5'-D(*AP*AP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3')
E: DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*AP*GP*AP*TP*TP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)27,9904
Polymers27,9904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PAIRED PROTEIN
F: DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3')

C: PAIRED PROTEIN
F: DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,9734
Polymers27,9734
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)72.210, 146.890, 77.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
DetailsA COMPLEX OF TWO HOMEODOMAINS (THE PROTEIN COMPONENT) BOUND TO ONE 14 BASE PAIR DNA DUPLEX IS THE MOLECULAR SPECIES ANALYZED IN THIS STUDY. EACH OF THE DNA DUPLEX AND THE COMPLEX HAS PSEUDO TWO-FOLD SYMMETRY ABOUT ITS CENTER. THE ASYMMETRIC UNIT CONTAINS 1.5 COMPLEXES, ONE OF WHICH IS COMPLETELY CONTAINED WITHIN THE ASYMMETRIC UNIT AND THE OTHER OF IS BISECTED AT ITS CENTER OF SYMMETRY BY A CRYSTALLOGRAPHIC TWO-FOLD AXIS. THE TWO-FOLD AVERAGED COMPLEX WAS MODELED AS A COMPLETE SINGLE HOMEODOMAIN AND A COMPLETE SINGLE STRAND OF THE DUPLEX. THEREFORE, THE MODEL CONTAINS THREE HOMEODOMAINS AND THREE DNA STRANDS.

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Components

#1: Protein PAIRED PROTEIN / PRD / PAIRED PROTEIN


Mass: 9716.782 Da / Num. of mol.: 3 / Fragment: HOMEODOMAIN / Mutation: C, C4S, S50Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P06601
#2: DNA chain DNA (5'-D(*AP*AP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3')


Mass: 4262.816 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*AP*GP*AP*TP*TP*AP*T)-3')


Mass: 4293.827 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3')


Mass: 4269.801 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE STANDARD HOMEODOMAIN NUMBERING SYSTEM (SEE, FOR EXAMPLE, KISSINGER, C.R., LIU, B., MARTIN- ...THE STANDARD HOMEODOMAIN NUMBERING SYSTEM (SEE, FOR EXAMPLE, KISSINGER, C.R., LIU, B., MARTIN-BLANCO, E., KORNBERG, T.B. AND PABO, C.O. (1990). CELL 63, 357 - 590) RELATES TO THE NUMBERING OF THE RESIDUES OF THE THREE HOMEODOMAINS IN THIS STRUCTURE IN THE FOLLOWING WAY: THE HOMEODOMAIN IS A 60 AMINO ACID MOTIF AND IS REFERRED TO HEREAFTER AS THE "HOMEODOMAIN PROPER". THE PROTEIN THAT WAS CRYSTALLIZED CONTAINS 17 ENDOGENOUS AMINO ACIDS UPSTREAM AND 4 AMINO ACIDS DOWNSTREAM OF THE 60 AMINO ACID HOMEODOMAIN PROPER. FOR EACH OF THE HOMEODOMAINS, THE RESIDUES ARE NUMBERED AS FOLLOWS, WITH SEGMENT IDENTIFIERS AS INDICATED: HOMEODOMAIN NO. 1: RESIDUES A 0 - A 64, WHERE RESIDUES A 1 - A 60 CORRESPOND TO THE HOMEODOMAIN PROPER. HOMEODOMAIN NO. 2: RESIDUES B 1 - B 58, WHERE RESIDUES B 1 - B 58 CORRESPOND TO THE HOMEODOMAIN PROPER (THE LAST 2 RESIDUES ARE DISORDERED AND SO NOT IN THE MODEL). HOMEODOMAIN NO. 3: RESIDUES C 0 - C 58, WHERE RESIDUES C 1 - C 58 CORRESPOND TO THE HOMEODOMAIN PROPER (THE LAST 2 RESIDUES ARE DISORDERED AND SO NOT IN THE MODEL).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1100 mMNa acetate11
220 mM11NaCl
319 %(w/v)PEG100011
413 %ethylene glycol112 % increments over 30 min.

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. obs: 28315 / % possible obs: 92.9 % / Num. measured all: 94960 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 83.3 % / Rmerge(I) obs: 0.185

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.198 / Rfactor obs: 0.198 / Highest resolution: 2 Å
Details: THE FOLLOWING SIDE CHAINS HAVE BEEN OMITTED FROM THE MODEL BECAUSE THEIR CONFORMATION WAS NOT EVIDENT FROM ELECTRON DENSITY MAPS: HOMEODOMAIN NO. 1: RESIDUES 122, 133, 158. HOMEODOMAIN NO. 2: ...Details: THE FOLLOWING SIDE CHAINS HAVE BEEN OMITTED FROM THE MODEL BECAUSE THEIR CONFORMATION WAS NOT EVIDENT FROM ELECTRON DENSITY MAPS: HOMEODOMAIN NO. 1: RESIDUES 122, 133, 158. HOMEODOMAIN NO. 2: RESIDUES 233, 236, 239, 255, 258. HOMEODOMAIN NO. 3: RESIDUES 300, 324, 357, 358. DUE TO THE TWO-FOLD AVERAGING OF THE DNA DUPLEXES, ALTERNATE SIDE CHAIN IDENTITIES HAVE BEEN MODELED IN THE FOLLOWING WAY: ALTERNATE SIDE CHAIN FOR RESIDUE A D 1A: RESIDUE T D 1B ALTERNATE SIDE CHAIN FOR RESIDUE T D 8A: RESIDUE A D 8B ALTERNATE SIDE CHAIN FOR RESIDUE T E 1A: RESIDUE A E 1B ALTERNATE SIDE CHAIN FOR RESIDUE A E 8A: RESIDUE T E 8B ALTERNATE SIDE CHAIN FOR RESIDUE T F 1A: RESIDUE A F 1B ALTERNATE SIDE CHAIN FOR RESIDUE T F 8A: RESIDUE A F 8B TWO OF THE WATER MOLECULES ARE EXCLUDED BY ONE OF THE TWO ALTERNATE SIDE CHAINS AT DNA RESIDUES NO. 408 AND 508, AS FOLLOWS: WATER RESIDUE NO. 941 IS PRESENT WITH THE ALTERNATE SIDE CHAIN REPRESENTED BY RESIDUE 508 BUT NOT 528. WATER RESIDUE NO. 942 IS PRESENT WITH THE ALTERNATE SIDE CHAIN REPRESENTED BY RESIDUE 428 BUT NOT 408.
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1530 966 0 243 2739
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na0.018
X-RAY DIFFRACTIONx_bond_d_prot0.012
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na2.8
X-RAY DIFFRACTIONx_angle_deg_prot1.51
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 6 Å / Rfactor obs: 0.197 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38 Å2

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