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- PDB-1bm8: DNA-BINDING DOMAIN OF MBP1 -

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Basic information

Entry
Database: PDB / ID: 1bm8
TitleDNA-BINDING DOMAIN OF MBP1
ComponentsTRANSCRIPTION FACTOR MBP1
KeywordsCELL CYCLE / CYCLINS / DNA SYNTHESIS / HELIX-TURN-HELIX DNA-BINDING DOMAIN / MULTIWAVELENGTH ANOMALOUS DIFFRACTION / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


Recruitment of mitotic centrosome proteins and complexes / equatorial microtubule organizing center / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / Recruitment of NuMA to mitotic centrosomes / spindle assembly / cytoplasmic microtubule organization / meiotic cell cycle / neuron migration ...Recruitment of mitotic centrosome proteins and complexes / equatorial microtubule organizing center / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / Recruitment of NuMA to mitotic centrosomes / spindle assembly / cytoplasmic microtubule organization / meiotic cell cycle / neuron migration / brain development / spindle pole / mitotic cell cycle / microtubule / centrosome / nucleoplasm / cytoplasm
Similarity search - Function
Transcription regulator HTH, APSES-type DNA-binding domain / KilA-N domain / Mlu1-box Binding Protein; DNA-binding Domain / Gamma tubulin complex component, C-terminal / Gamma-tubulin complex component, C-terminal domain superfamily / Gamma tubulin complex component C-terminal / Gamma-tubulin complex component protein / Gamma tubulin complex component protein, N-terminal / Gamma tubulin complex component N-terminal / Roll / Alpha Beta
Similarity search - Domain/homology
Gamma-tubulin complex component
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.71 Å
AuthorsXu, R.-M. / Koch, C. / Liu, Y. / Horton, J.R. / Knapp, D. / Nasmyth, K. / Cheng, X.
CitationJournal: Structure / Year: 1997
Title: Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis.
Authors: Xu, R.M. / Koch, C. / Liu, Y. / Horton, J.R. / Knapp, D. / Nasmyth, K. / Cheng, X.
History
DepositionJul 29, 1998Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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
A: TRANSCRIPTION FACTOR MBP1


Theoretical massNumber of molelcules
Total (without water)11,4871
Polymers11,4871
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.350, 43.350, 124.220
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 TRANSCRIPTION FACTOR MBP1 / MCB (MLUI CELL-CYLE BOX) BINDING PROTEIN


Mass: 11487.209 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cell line: BL21 / Plasmid: BL21 (DE3) PLYSS/PET43 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P39678
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 34 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Details: drop contains equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2300 mM1dropNaCl
350 mMsodium phosphate1drop
470 %satsodium citrate1reservoir
5100 mMimidazole1reservoir

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.96 / Wavelength: 0.96, 1.54
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961
21.541
ReflectionResolution: 1.7→30 Å / Num. obs: 12811 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.4
Reflection shellResolution: 1.71→1.78 Å / % possible all: 34
Reflection
*PLUS
Num. measured all: 68232
Reflection shell
*PLUS
% possible obs: 34 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.71→5 Å / Isotropic thermal model: RESTRAINED / σ(F): 0
Details: ISOTROPIC THERMAL FACTOR RESTRAINTS: 36. (A**2) FOR MAIN-CHAIN BONDS AND 40.3 (A**2) FOR SIDE-CHAIN BONDS.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 -10 %RANDOM
Rwork0.197 ---
obs0.197 10273 93.6 %-
Displacement parametersBiso mean: 36 Å2
Refine analyzeLuzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.71→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 0 0 66 878
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.11
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.98
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
LS refinement shellResolution: 1.71→1.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.335 -10 %
Rwork0.402 535 -
obs--34.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.98
LS refinement shell
*PLUS
Rfactor obs: 0.402

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