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- PDB-5nm9: Crystal structure of the placozoa Trichoplax adhaerens Smad4-MH1 ... -

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Basic information

Entry
Database: PDB / ID: 5nm9
TitleCrystal structure of the placozoa Trichoplax adhaerens Smad4-MH1 bound to the GGCGC site.
Components
  • DNA (5'-D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3')
  • Mothers against decapentaplegic homolog
KeywordsTRANSCRIPTION / Smads / transcription factor / DNA complex
Function / homology
Function and homology information


heteromeric SMAD protein complex / SMAD protein signal transduction / I-SMAD binding / anatomical structure morphogenesis / BMP signaling pathway / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / metal ion binding / cytoplasm
Similarity search - Function
Smad3; Chain A / SMAD MH1 domain / 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 ...Smad3; Chain A / SMAD MH1 domain / 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 / SMAD/FHA domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Mothers against decapentaplegic homolog
Similarity search - Component
Biological speciesTrichoplax adhaerens (invertebrata)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsKaczmarska, Z. / Freier, R. / Marquez, J.A. / Macias, M.J.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors.
Authors: Martin-Malpartida, P. / Batet, M. / Kaczmarska, Z. / Freier, R. / Gomes, T. / Aragon, E. / Zou, Y. / Wang, Q. / Xi, Q. / Ruiz, L. / Vea, A. / Marquez, J.A. / Massague, J. / Macias, M.J.
History
DepositionApr 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Mothers against decapentaplegic homolog
B: Mothers against decapentaplegic homolog
C: DNA (5'-D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3')
D: DNA (5'-D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1396
Polymers43,0084
Non-polymers1312
Water34219
1
A: Mothers against decapentaplegic homolog
C: DNA (5'-D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3')
D: DNA (5'-D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3')
hetero molecules

B: Mothers against decapentaplegic homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1396
Polymers43,0084
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
2
B: Mothers against decapentaplegic homolog
hetero molecules

A: Mothers against decapentaplegic homolog
C: DNA (5'-D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3')
D: DNA (5'-D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1396
Polymers43,0084
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Unit cell
Length a, b, c (Å)37.150, 76.980, 145.040
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 Mothers against decapentaplegic homolog / Smad4 / Mothers against DPP homolog / SMAD family member


Mass: 15985.443 Da / Num. of mol.: 2 / Fragment: MH1 domain, UNP residues 33-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax adhaerens (invertebrata) / Gene: TRIADDRAFT_30731 / Production host: Escherichia coli (E. coli) / References: UniProt: B3S7S5
#2: DNA chain DNA (5'-D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3')


Mass: 5518.555 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 4.8% PEG 4000, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 77.62 Å2
Reflection shellResolution: 2.43→2.44 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 204 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MEY

5mey


Resolution: 2.43→29.46 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.369 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.39 / SU Rfree Blow DPI: 0.248 / SU Rfree Cruickshank DPI: 0.246
RfactorNum. reflection% reflectionSelection details
Rfree0.251 786 4.85 %RANDOM
Rwork0.221 ---
obs0.222 16190 98.8 %-
Displacement parametersBiso mean: 82.04 Å2
Baniso -1Baniso -2Baniso -3
1--8.6596 Å20 Å20 Å2
2--1.7698 Å20 Å2
3---6.8898 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 2.43→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 738 2 19 2656
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012763HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.023894HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d844SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes41HARMONIC2
X-RAY DIFFRACTIONt_gen_planes324HARMONIC5
X-RAY DIFFRACTIONt_it2763HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion22.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion364SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2750SEMIHARMONIC4
LS refinement shellResolution: 2.43→2.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.233 122 4.22 %
Rwork0.228 2772 -
all0.228 2894 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5264-0.1678-0.80547.76241.06528.5836-0.1143-0.05790.21410.4163-0.03680.2776-0.26340.1420.15110.0691-0.01180.0078-0.2818-0.0008-0.1319-13.093213.9927-20.1989
23.3699-0.03240.61435.76380.10076.3020.1747-0.126-0.18160.2771-0.0234-0.39410.26180.0397-0.15140.2634-0.0135-0.0776-0.2852-0.0008-0.136-13.048846.0105-19.9128
36.0263-4.127-1.274211.84192.31954.6894-0.0386-0.2935-0.04270.77020.5280.20980.94740.4699-0.48940.25020.00640.304-0.3651-0.1277-0.2904-12.5091-9.9977-20.1817
46.6782-3.3319-1.1486.71110.16063.56490.1912-0.48640.47051.0260.6374-0.1609-0.1036-0.1666-0.82860.5057-0.00740.304-0.3469-0.0687-0.2042-13.2886-8.7672-19.4949
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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