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- PDB-1gv2: CRYSTAL STRUCTURE OF C-MYB R2R3 -

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Basic information

Entry
Database: PDB / ID: 1gv2
TitleCRYSTAL STRUCTURE OF C-MYB R2R3
ComponentsMYB PROTO-ONCOGENE PROTEIN
KeywordsTRANSCRIPTION / MYB / C-MYB / DNA BINDING / ION BINDING
Function / homology
Function and homology information


positive regulation of testosterone secretion / positive regulation of hepatic stellate cell proliferation / myeloid cell development / positive regulation of transforming growth factor beta production / positive regulation of hepatic stellate cell activation / negative regulation of hematopoietic progenitor cell differentiation / skeletal muscle cell proliferation / embryonic digestive tract development / myeloid cell differentiation / cellular response to interleukin-6 ...positive regulation of testosterone secretion / positive regulation of hepatic stellate cell proliferation / myeloid cell development / positive regulation of transforming growth factor beta production / positive regulation of hepatic stellate cell activation / negative regulation of hematopoietic progenitor cell differentiation / skeletal muscle cell proliferation / embryonic digestive tract development / myeloid cell differentiation / cellular response to interleukin-6 / T-helper 2 cell differentiation / WD40-repeat domain binding / stem cell division / positive regulation of collagen biosynthetic process / homeostasis of number of cells / positive regulation of glial cell proliferation / negative regulation of megakaryocyte differentiation / spleen development / cellular response to retinoic acid / positive regulation of smooth muscle cell proliferation / thymus development / cellular response to leukemia inhibitory factor / B cell differentiation / response to ischemia / erythrocyte differentiation / G1/S transition of mitotic cell cycle / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / cellular response to hydrogen peroxide / calcium ion transport / positive regulation of neuron apoptotic process / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / response to hypoxia / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / 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
Transcriptional activator Myb
Similarity search - Component
Biological speciesMus Musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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.
History
DepositionFeb 5, 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 1.3Oct 31, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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)12,7213
Polymers12,6751
Non-polymers462
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.722, 28.250, 44.129
Angle α, β, γ (deg.)90.00, 90.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MYB PROTO-ONCOGENE PROTEIN / C-MYB


Mass: 12674.693 Da / Num. of mol.: 1 / Fragment: R2R3, RESIDUES 89-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus Musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06876
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: 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: 1.9 Å3/Da / Density % sol: 35.4 %
Crystal growpH: 6.8
Details: 1.6-1.7 M SODIUM CITRATE PH 6.8, PROTEIN CONCENTRATION 15 MG/ML, CRYSTAL WAS GROWN BY REPEATED MACROSEEDING, TRANSFORMED TO LOW HUMIDITY FORM AND FLASH COOLED, 1-2% V/V OF GLYCEROL WAS ADDED ...Details: 1.6-1.7 M SODIUM CITRATE PH 6.8, PROTEIN CONCENTRATION 15 MG/ML, CRYSTAL WAS GROWN BY REPEATED MACROSEEDING, TRANSFORMED TO LOW HUMIDITY FORM AND FLASH COOLED, 1-2% V/V OF GLYCEROL WAS ADDED TO SODIUM CITRATE TO PREVENT THE CRYSTAL CRACKING DURING THE FLASH COOLING

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 29, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 11033 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.244 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.601
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 3.53 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 1.904 / % possible all: 97.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1MBG AND 1MBJ

1mbg

1mbj


Resolution: 1.68→44.12 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 87837.03 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.21 570 5.2 %RANDOM
Rwork0.193 ---
obs0.193 11022 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.1365 Å2 / ksol: 0.357663 e/Å3
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20.64 Å2
2--0.17 Å20 Å2
3----1.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-50 Å
Luzzati sigma a0.21 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.68→44.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms867 0 2 60 929
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.741.5
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_scbond_it3.212
X-RAY DIFFRACTIONc_scangle_it4.922.5
LS refinement shellResolution: 1.68→1.79 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 77 4.3 %
Rwork0.31 1702 -
obs--96.9 %
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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