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- PDB-1an2: RECOGNITION BY MAX OF ITS COGNATE DNA THROUGH A DIMERIC B/HLH/Z DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1an2
TitleRECOGNITION BY MAX OF ITS COGNATE DNA THROUGH A DIMERIC B/HLH/Z DOMAIN
Components
  • DNA (5'-D(*GP*TP*GP*TP*AP*GP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*C P*TP*AP*CP*AP*C)- 3')
  • PROTEIN (TRANSCRIPTION FACTOR MAX (TF MAX))
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


Mad-Max complex / Myc-Max complex / Transcription of E2F targets under negative control by DREAM complex / E-box binding / Transcriptional Regulation by E2F6 / MLL1 complex / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / protein-DNA complex / DNA-binding transcription repressor activity, RNA polymerase II-specific ...Mad-Max complex / Myc-Max complex / Transcription of E2F targets under negative control by DREAM complex / E-box binding / Transcriptional Regulation by E2F6 / MLL1 complex / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / protein-DNA complex / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / DNA-binding transcription factor binding / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / dendrite / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein max
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsFerre-D'Amare, A.R. / Prendergast, G.C. / Ziff, E.B. / Burley, S.K.
CitationJournal: Nature / Year: 1993
Title: Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain.
Authors: Ferre-D'Amare, A.R. / Prendergast, G.C. / Ziff, E.B. / Burley, S.K.
History
DepositionSep 6, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2013Group: Version format compliance
Revision 1.4Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Feb 7, 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
B: DNA (5'-D(*GP*TP*GP*TP*AP*GP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*C P*TP*AP*CP*AP*C)- 3')
A: PROTEIN (TRANSCRIPTION FACTOR MAX (TF MAX))


Theoretical massNumber of molelcules
Total (without water)16,9752
Polymers16,9752
Non-polymers00
Water0
1
B: DNA (5'-D(*GP*TP*GP*TP*AP*GP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*C P*TP*AP*CP*AP*C)- 3')
A: PROTEIN (TRANSCRIPTION FACTOR MAX (TF MAX))

B: DNA (5'-D(*GP*TP*GP*TP*AP*GP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*C P*TP*AP*CP*AP*C)- 3')
A: PROTEIN (TRANSCRIPTION FACTOR MAX (TF MAX))


Theoretical massNumber of molelcules
Total (without water)33,9504
Polymers33,9504
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area7300 Å2
ΔGint-54 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.200, 72.200, 146.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: DNA chain DNA (5'-D(*GP*TP*GP*TP*AP*GP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*C P*TP*AP*CP*AP*C)- 3')


Mass: 6752.366 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Protein PROTEIN (TRANSCRIPTION FACTOR MAX (TF MAX))


Mass: 10222.484 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Keywords: FRAGMENT: DNA BINDING DOMAIN / References: UniProt: P61244

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 61.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: pH 5.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 100011
3GLYCEROL11
4KCL11
5MGCL211
6NA CACODYLATE11
7WATER12
8PEG 100012
9GLYCEROL12
10KCL12
11MGCL212
12NA CACODYLATE12
Crystal grow
*PLUS
Temperature: 4 ℃ / PH range low: 5.75 / PH range high: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.5-7.5 %PEG10001reservoir
25-10 %glycerol1reservoir
3100 mM1reservoirKCl
42 mM1reservoirMgCl2
5100 mMsodium cacodylate1reservoir
61
71
81
91
101
111
121

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Data collection

DiffractionMean temperature: 258 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1
DetectorDetector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 21448 / Num. obs: 4507 / % possible obs: 85.3 % / Rsym value: 0.065 / Net I/σ(I): 13.9
Reflection shellResolution: 2.9→3 Å / % possible all: 61
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / % possible obs: 85.3 % / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 61 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.96

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.9→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.232 -
obs0.232 3916
Refinement stepCycle: LAST / Resolution: 2.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms717 448 0 0 1165
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 6 Å / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg2.4

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