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- PDB-1gvd: CRYSTAL STRUCTURE OF C-MYB R2 V103L MUTANT -

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Basic information

Entry
Database: PDB / ID: 1gvd
TitleCRYSTAL STRUCTURE OF C-MYB R2 V103L MUTANT
ComponentsMYB PROTO-ONCOGENE PROTEIN
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / MYB / C-MYB / DNA BINDING / ION BINDING / PROTO-ONCOGENE / NUCLEAR PROTEIN
Function / homology
Function and homology information


myeloid cell development / embryonic digestive tract development / myeloid cell differentiation / stem cell division / cellular response to interleukin-6 / WD40-repeat domain binding / homeostasis of number of cells / spleen development / B cell differentiation / cellular response to leukemia inhibitory factor ...myeloid cell development / embryonic digestive tract development / myeloid cell differentiation / stem cell division / cellular response to interleukin-6 / WD40-repeat domain binding / homeostasis of number of cells / spleen development / B cell differentiation / cellular response to leukemia inhibitory factor / thymus development / G1/S transition of mitotic cell cycle / RNA polymerase II transcription regulator complex / calcium ion transport / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / : / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Homeodomain-like ...Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / : / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Homeodomain-like / SANT/Myb domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
AMMONIUM ION / Transcriptional activator Myb
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsTahirov, T.H. / Ogata, K.
Citation
Journal: To be Published
Title: Crystal Structure of C-Myb DNA-Binding Domain: Specific Na+ Binding and Correlation with NMR Structure
Authors: Tahirov, T.H. / Morii, H. / Uedaira, H. / Sasaki, M. / Sarai, A. / Adachi, S. / Park, S.Y. / Kamiya, N. / Ogata, K.
#1: Journal: Cell (Cambridge,Mass.) / Year: 2002
Title: Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter
Authors: Tahirov, T.H. / Sato, K. / Ichikawa-Iwata, E. / Sasaki, M. / Inoue-Bungo, T. / Shiina, M. / Kimura, K. / Takata, S. / Fujikawa, A. / Morii, H. / Kumasaka, T. / Yamamoto, M. / Ishii, S. / Ogata, K.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-Ray Analysis of Wild Type and V103L Mutant Myb R2 DNA-Binding Domain
Authors: Tahirov, T.H. / Morii, H. / Uedaira, H. / Sarai, A. / Ogata, K.
History
DepositionFeb 8, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYB PROTO-ONCOGENE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5274
Polymers6,3161
Non-polymers2103
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)28.951, 40.114, 48.807
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: Protein MYB PROTO-ONCOGENE PROTEIN


Mass: 6316.437 Da / Num. of mol.: 1 / Fragment: R2, RESIDUES 90-141 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P06876
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION VAL 103 LEU

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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: 2.24 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 297 K / pH: 6.8
Details: 3.15 M AMMONIUM SULFATE IN 0.05 M MES BUFFER AT PH 6.8, PROTEIN CONCENTRATION 10 MG/ML PLUS 10 MM DTT, TEMPERATURE 297 K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MAC SCIENCE M06XHF22 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Jul 16, 1997 / Details: MAC SCIENCE DOUBLE MIRROR
RadiationMonochromator: 0.15 MM NICKEL FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. obs: 10332 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 8.657 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 38.204
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 6.07 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 8.351 / % possible all: 95.2

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GV5

1gv5


Resolution: 1.45→12.45 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 731165.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.195 543 5.3 %RANDOM
Rwork0.18 ---
obs0.18 10307 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.5097 Å2 / ksol: 0.550446 e/Å3
Displacement parametersBiso mean: 16.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2---1.24 Å20 Å2
3---0.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-20 Å
Luzzati sigma a0.07 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.45→12.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms446 0 11 51 508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.941.5
X-RAY DIFFRACTIONc_mcangle_it2.82
X-RAY DIFFRACTIONc_scbond_it3.212
X-RAY DIFFRACTIONc_scangle_it4.742.5
LS refinement shellResolution: 1.45→1.54 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 61 3.8 %
Rwork0.236 1543 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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