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- PDB-1md0: CRYSTAL STRUCTURE OF AN INHIBITED FRAGMENT OF Ets-1 -

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Basic information

Entry
Database: PDB / ID: 1md0
TitleCRYSTAL STRUCTURE OF AN INHIBITED FRAGMENT OF Ets-1
ComponentsC-ets-1 protein
KeywordsTRANSCRIPTION / AUTOINHIBITION / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


Oncogene Induced Senescence / regulation of extracellular matrix disassembly / histone acetyltransferase binding / immune system process / regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / negative regulation of inflammatory response / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding ...Oncogene Induced Senescence / regulation of extracellular matrix disassembly / histone acetyltransferase binding / immune system process / regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / negative regulation of inflammatory response / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / DNA-binding transcription factor activity / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. ...Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGarvie, C.W. / Pufall, M.A. / Graves, B.J. / Wolberger, C.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structural Analysis of the Autoinhibition of Ets-1 and Its Role in Protein Partnerships
Authors: Garvie, C.W. / Pufall, M.A. / Graves, B.J. / Wolberger, C.
History
DepositionAug 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

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Assembly

Deposited unit
A: C-ets-1 protein
B: C-ets-1 protein


Theoretical massNumber of molelcules
Total (without water)32,7312
Polymers32,7312
Non-polymers00
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-11 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.350, 66.670, 83.510
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 C-ets-1 protein / p54


Mass: 16365.706 Da / Num. of mol.: 2 / Fragment: ETS domain, Residues 300-440
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ETS-1 / Plasmid: PET21D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27577
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM Sodium Citrate, 20% Peg4000, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.27 mMprotein1drop
250 mM1dropNaCl
310 mMTris1droppH8.0
450 mMsodium citrate1reservoir
5100 mMMES1reservoirpH6.5
620 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5415 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 2001 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5415 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 20820 / Num. obs: 19649 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 21.4
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1396 / Rsym value: 0.176 / % possible all: 68.3
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 68.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K79

1k79


Resolution: 2→41.76 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1491684.06 / Data cutoff high rms absF: 1491684.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 947 4.8 %RANDOM
Rwork0.209 ---
all-20545 --
obs-19598 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.4987 Å2 / ksol: 0.357966 e/Å3
Displacement parametersBiso mean: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.42 Å20 Å20 Å2
2---1.87 Å20 Å2
3---5.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 0 253 2664
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 101 4 %
Rwork0.258 2443 -
obs--74.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.12
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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