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- PDB-1pdn: CRYSTAL STRUCTURE OF A PAIRED DOMAIN-DNA COMPLEX AT 2.5 ANGSTROMS... -

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Basic information

Entry
Database: PDB / ID: 1pdn
TitleCRYSTAL STRUCTURE OF A PAIRED DOMAIN-DNA COMPLEX AT 2.5 ANGSTROMS RESOLUTION REVEALS STRUCTURAL BASIS FOR PAX DEVELOPMENTAL MUTATIONS
Components
  • DNA (5'-D(*AP*AP*CP*GP*TP*CP*AP*CP*GP*GP*TP*TP*GP*AP*C)-3')
  • DNA (5'-D(*TP*TP*GP*TP*CP*AP*AP*CP*CP*GP*TP*GP*AP*CP*G)-3')
  • PROTEIN (PRD PAIRED)
KeywordsGENE REGULATION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / PAX / PRD / PAIRED DOMAIN / DNA-BINDING PROTEIN / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


periodic partitioning by pair rule gene / HATs acetylate histones / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nervous system development / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / 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: 2.5 Å
AuthorsXu, W. / Rould, M.A. / Jun, S. / Desplan, C. / Pabo, C.O.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1995
Title: Crystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations.
Authors: Xu, W. / Rould, M.A. / Jun, S. / Desplan, C. / Pabo, C.O.
History
DepositionMay 16, 1995Deposition site: BNL / Processing site: BNL
Revision 1.0Jul 31, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*AP*CP*GP*TP*CP*AP*CP*GP*GP*TP*TP*GP*AP*C)-3')
B: DNA (5'-D(*TP*TP*GP*TP*CP*AP*AP*CP*CP*GP*TP*GP*AP*CP*G)-3')
C: PROTEIN (PRD PAIRED)


Theoretical massNumber of molelcules
Total (without water)23,3833
Polymers23,3833
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.600, 68.600, 100.500
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: DNA chain DNA (5'-D(*AP*AP*CP*GP*TP*CP*AP*CP*GP*GP*TP*TP*GP*AP*C)-3')


Mass: 4593.999 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*TP*GP*TP*CP*AP*AP*CP*CP*GP*TP*GP*AP*CP*G)-3')


Mass: 4584.984 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (PRD PAIRED)


Mass: 14204.399 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: PRD / Plasmid: PET14BPRDPDB / Gene (production host): PRD / Production host: BL21(DE3) / References: UniProt: P06601
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.82 Å3/Da / Density % sol: 68 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2BIS-TRIS-PROPANE11
3PEG 100011
4NH4 ACETATE11
5MGCL211
6EDTA11
7DTT11
8WATER12
9PEG 100012
10DTT12
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-IDChemical formula
10.49 mMprd paired domain1drop
20.62 mMDNA complex1drop
30.15-0.2 Mammonium acetate1drop
410 mMbis-tris-propane1drop
510 mM1dropMgCl2
60.1 mM1drop
7mMdithiothreitol1drop
85 %PEG10001drop
910 %PEG10001reservoir
105 mMdithiothreitol1reservoir

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 1, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 40156 / Num. obs: 9285 / Redundancy: 4.68 % / Rmerge(I) obs: 0.075
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % possible obs: 92.5 % / Num. measured all: 40156

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
RefinementResolution: 2.5→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.284 -10 %
Rwork0.234 --
obs0.234 9285 92.5 %
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms912 609 0 13 1534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.8
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
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.8

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