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- PDB-6m75: C-Myc DNA binding protein complex -

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Basic information

Entry
Database: PDB / ID: 6m75
TitleC-Myc DNA binding protein complex
Components
  • DNA (5'-D(*TP*CP*TP*TP*AP*TP*T)-3')
  • RNA-binding motif, single-stranded-interacting protein 1
KeywordsDNA BINDING PROTEIN/DNA / c-myc / promoter binding / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


poly(A) binding / poly(U) RNA binding / RNA processing / mRNA 3'-UTR binding / single-stranded DNA binding / double-stranded DNA binding / DNA replication / ribonucleoprotein complex / RNA binding / nucleus / cytosol
Similarity search - Function
MSSP-1, RNA recognition motif 1 / Paraneoplastic encephalomyelitis antigen / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
DNA / RNA-binding motif, single-stranded-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsAggarwal, P. / Bhavesh, N.S.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Hinge like domain motion facilitates human RBMS1 protein binding to proto-oncogene c-myc promoter.
Authors: Aggarwal, P. / Bhavesh, N.S.
History
DepositionMar 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 2.0Jun 22, 2022Group: Database references / Polymer sequence / Category: database_2 / entity_poly
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.type
Revision 2.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding motif, single-stranded-interacting protein 1
C: DNA (5'-D(*TP*CP*TP*TP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,11712
Polymers20,1562
Non-polymers96110
Water57632
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, stoichiometry gave 1:1 binding
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-107 kcal/mol
Surface area11180 Å2
Unit cell
Length a, b, c (Å)83.680, 114.946, 27.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein RNA-binding motif, single-stranded-interacting protein 1 / Single-stranded DNA-binding protein MSSP-1 / Suppressor of CDC2 with RNA-binding motif 2


Mass: 18077.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBMS1, C2orf12, MSSP, MSSP1, SCR2 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29558
#2: DNA chain DNA (5'-D(*TP*CP*TP*TP*AP*TP*T)-3')


Mass: 2078.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.27 Å3/Da / Density % sol: 59.72 % / Description: THIN plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.07 M HEPES pH 7.5, 0.05 M Magnesium Sulfate, 1.8 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.56→67.65 Å / Num. obs: 9032 / % possible obs: 99.7 % / Redundancy: 9.7 % / Biso Wilson estimate: 38.7 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.055 / Rrim(I) all: 0.175 / Net I/σ(I): 11.9
Reflection shellResolution: 2.57→2.61 Å / Redundancy: 10 % / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 428 / CC1/2: 0.711 / Rpim(I) all: 0.328 / Rrim(I) all: 1.052 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
autoPROCdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FXL

1fxl


Resolution: 2.57→19.66 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 900 10 %RANDOM
Rwork0.2112 8099 --
obs0.2137 8999 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.7 Å2 / Biso mean: 48.9707 Å2 / Biso min: 15.3 Å2
Refinement stepCycle: final / Resolution: 2.57→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 120 50 32 1466
Biso mean--78.78 37.54 -
Num. residues----173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.57-2.730.34881310.27681335146699
2.73-2.940.27741480.269413021450100
2.94-3.230.29471450.260513241469100
3.23-3.690.23881400.200113481488100
3.7-4.650.1881610.168713671528100
4.65-19.660.21531750.194414231598100
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)
13.8466-1.32161.79844.9513-2.84647.2334-0.02530.0481-0.1073-0.23490.09480.21780.1863-0.5963-0.08190.169-0.00150.02510.2894-0.02660.159137.246112.480935.6453
26.7848-6.914-5.95038.22377.06746.32260.12010.49380.6647-0.26090.6537-1.074-0.24490.404-0.47630.4969-0.18460.01570.54250.01630.465346.563815.633428.5717
37.79033.2108-0.65599.2722.31135.2320.6134-0.2899-1.09420.5715-0.5303-1.24350.41190.0193-0.12740.3498-0.1471-0.13210.5080.03110.485865.893218.676414.0664
48.95210.63742.24392.0679-3.34277.1693-0.1078-0.0860.14-0.0747-0.074-0.6295-0.96720.8265-0.04640.2979-0.08320.08040.4534-0.04940.430651.074616.799638.264
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 68 )A1 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 84 )A69 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 167 )A85 - 167
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 6 )C1 - 6

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