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- PDB-1mb1: MBP1 FROM SACCHAROMYCES CEREVISIAE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1mb1
TitleMBP1 FROM SACCHAROMYCES CEREVISIAE
ComponentsMLU1-BOX BINDING PROTEIN
KeywordsTRANSCRIPTION REGULATION / CELL-CYCLE / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


MBF transcription complex / SBF transcription complex / G1/S transition of mitotic cell cycle / maintenance of translational fidelity / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Transcription regulator HTH, APSES-type DNA-binding domain / KilA-N domain / : / Transcription regulator HTH, APSES-type DNA-binding domain / KilA, N-terminal/APSES-type HTH, DNA-binding / HTH APSES-type DNA-binding domain superfamily / APSES-type HTH DNA-binding domain profile. / KilA-N / Mlu1-box Binding Protein; DNA-binding Domain / Ankyrin repeats (many copies) ...Transcription regulator HTH, APSES-type DNA-binding domain / KilA-N domain / : / Transcription regulator HTH, APSES-type DNA-binding domain / KilA, N-terminal/APSES-type HTH, DNA-binding / HTH APSES-type DNA-binding domain superfamily / APSES-type HTH DNA-binding domain profile. / KilA-N / Mlu1-box Binding Protein; DNA-binding Domain / Ankyrin repeats (many copies) / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Transcription factor MBP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsTaylor, I.A. / Smerdon, S.J.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: The X-ray structure of the DNA-binding domain from the Saccharomyces cerevisiae cell-cycle transcription factor Mbp1 at 2.1 A resolution.
Authors: Taylor, I.A. / Treiber, M.K. / Olivi, L. / Smerdon, S.J.
History
DepositionJul 23, 1997Processing site: BNL
Revision 1.0Jul 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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: MLU1-BOX BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,9011
Polymers14,9011
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.580, 42.580, 123.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein MLU1-BOX BINDING PROTEIN / MBP1


Mass: 14900.885 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cell line: BL21 / Cellular location: NUCLEAR / Plasmid: PET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P39678
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.88 Å3/Da / Density % sol: 28 %
Crystal growpH: 6.9 / Details: pH 6.9
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: Taylor, I.A., (1997) Proteins Struct. Funct. Genet., 27,325.
PH range low: 8.2 / PH range high: 7.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
128-30 %(w/v)PEG33501reservoir
250 mMTris-HCl1reservoir
3200 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.22
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jan 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.22 Å / Relative weight: 1
ReflectionResolution: 2.1→18 Å / Num. obs: 6810 / % possible obs: 94.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 30
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 11 / % possible all: 93.3

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Processing

Software
NameClassification
MLPHAREphasing
CCP4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→7 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29 353 5 %RANDOM
Rwork0.215 ---
obs-6469 95 %-
Displacement parametersBiso mean: 27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms790 0 0 60 850
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_deg / Dev ideal: 2.47

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