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- PDB-3gmj: Crystal structure of MAD MH2 domain -

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Basic information

Entry
Database: PDB / ID: 3gmj
TitleCrystal structure of MAD MH2 domain
ComponentsProtein mothers against dpp
KeywordsTRANSCRIPTION / MH2 / SMAD / MAD / Cytoplasm / Developmental protein / Nucleus / Phosphoprotein / Transcription regulation / Ubl conjugation
Function / homology
Function and homology information


Signaling by BMP / RUNX2 regulates bone development / imaginal disc morphogenesis / R8 cell fate specification / histoblast morphogenesis / negative regulation of salivary gland boundary specification / imaginal disc-derived wing vein morphogenesis / trunk segmentation / imaginal disc-derived leg morphogenesis / germ-line stem cell division ...Signaling by BMP / RUNX2 regulates bone development / imaginal disc morphogenesis / R8 cell fate specification / histoblast morphogenesis / negative regulation of salivary gland boundary specification / imaginal disc-derived wing vein morphogenesis / trunk segmentation / imaginal disc-derived leg morphogenesis / germ-line stem cell division / compound eye morphogenesis / positive regulation of neuromuscular junction development / follicle cell of egg chamber development / wing disc anterior/posterior pattern formation / positive regulation of synaptic assembly at neuromuscular junction / Ub-specific processing proteases / RNA polymerase II transcription repressor complex / intestinal stem cell homeostasis / ventral cord development / co-SMAD binding / heteromeric SMAD protein complex / imaginal disc-derived wing morphogenesis / germ-line stem cell population maintenance / SMAD protein signal transduction / I-SMAD binding / negative regulation of G1/S transition of mitotic cell cycle / regulation of cell differentiation / somatic stem cell population maintenance / anatomical structure morphogenesis / BMP signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tumour Suppressor Smad4 - #10 / MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type ...Tumour Suppressor Smad4 - #10 / MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain / Domain A in dwarfin family proteins / SMAD-like domain superfamily / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein mothers against dpp
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWu, J.W. / Wang, C.
CitationJournal: SCI.CHINA, SER.C: LIFE SCI. / Year: 2009
Title: Crystal structure of the MH2 domain of Drosophila Mad
Authors: Wang, C. / Chen, L. / Wang, L. / Wu, J.W.
History
DepositionMar 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Protein mothers against dpp
B: Protein mothers against dpp
A: Protein mothers against dpp
C: Protein mothers against dpp


Theoretical massNumber of molelcules
Total (without water)108,2604
Polymers108,2604
Non-polymers00
Water43224
1
D: Protein mothers against dpp

D: Protein mothers against dpp

D: Protein mothers against dpp


Theoretical massNumber of molelcules
Total (without water)81,1953
Polymers81,1953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6970 Å2
ΔGint-29 kcal/mol
Surface area24430 Å2
MethodPISA
2
B: Protein mothers against dpp
A: Protein mothers against dpp
C: Protein mothers against dpp


Theoretical massNumber of molelcules
Total (without water)81,1953
Polymers81,1953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-25 kcal/mol
Surface area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.261, 137.261, 194.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Protein mothers against dpp


Mass: 27065.055 Da / Num. of mol.: 4 / Fragment: MH2 domain, residues 215-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Mad / Plasmid: pPGH / Production host: Escherichia coli (E. coli) / References: UniProt: P42003
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONFLICT HAS BEEN GENERATED IN CLONING PROCESS.

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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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15%(v/v) Methanol, 0.3M Na Malonate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.849
ReflectionResolution: 2.8→50 Å / Num. obs: 33568 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.9 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→22.328 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.832 / σ(F): 1.97 / Phase error: 24.58 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1702 5.07 %random
Rwork0.179 ---
obs0.181 33566 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.7 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 149.46 Å2 / Biso mean: 77.239 Å2 / Biso min: 29.56 Å2
Baniso -1Baniso -2Baniso -3
1--9.73 Å2-0 Å20 Å2
2---9.73 Å2-0 Å2
3---5.723 Å2
Refinement stepCycle: LAST / Resolution: 2.8→22.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6224 0 0 24 6248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086388
X-RAY DIFFRACTIONf_angle_d1.098689
X-RAY DIFFRACTIONf_chiral_restr0.071934
X-RAY DIFFRACTIONf_plane_restr0.0041139
X-RAY DIFFRACTIONf_dihedral_angle_d19.2742240
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8-2.8570.3341040.28218731977
2.857-2.9190.2951000.27618861986
2.919-2.9870.286900.26818771967
2.987-3.0610.312890.25818731962
3.061-3.1440.288870.23818751962
3.144-3.2360.254990.23219012000
3.236-3.340.2641130.23318421955
3.34-3.4590.2151060.20518921998
3.459-3.5970.2381120.19818581970
3.597-3.760.2171130.18418461959
3.76-3.9570.2231010.16618971998
3.957-4.2030.2041040.15618521956
4.203-4.5250.177970.14218691966
4.525-4.9760.168970.13918971994
4.976-5.6860.199990.15418951994
5.686-7.1250.2471010.18518561957
7.125-22.3280.169890.13318761965

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