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- PDB-6v4g: Crystal Structure Analysis of Zebra fish MDMX -

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Basic information

Entry
Database: PDB / ID: 6v4g
TitleCrystal Structure Analysis of Zebra fish MDMX
Components
  • Protein Mdm4
  • Stapled peptide QSQQTF(0EH)NLWRLE(MK8)QN(NH2)
KeywordsAPOPTOSIS / p53 binding
Function / homology
Function and homology information


Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Stabilization of p53 / Ub-specific processing proteases / ubiquitin-protein transferase activity / regulation of cell cycle / protein ubiquitination / negative regulation of apoptotic process ...Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Stabilization of p53 / Ub-specific processing proteases / ubiquitin-protein transferase activity / regulation of cell cycle / protein ubiquitination / negative regulation of apoptotic process / nucleus / metal ion binding
Similarity search - Function
MDM4 / MDM2 / SWIB/MDM2 domain / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. ...MDM4 / MDM2 / SWIB/MDM2 domain / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Structure / Year: 2020
Title: Identification of a Structural Determinant for Selective Targeting of HDMX.
Authors: Ben-Nun, Y. / Seo, H.S. / Harvey, E.P. / Hauseman, Z.J. / Wales, T.E. / Newman, C.E. / Cathcart, A.M. / Engen, J.R. / Dhe-Paganon, S. / Walensky, L.D.
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
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 1.2Oct 11, 2023Group: 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Mdm4
B: Stapled peptide QSQQTF(0EH)NLWRLE(MK8)QN(NH2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3133
Polymers14,2172
Non-polymers961
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-20 kcal/mol
Surface area5770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.290, 108.930, 30.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

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Components

#1: Protein Protein Mdm4 / Double minute 4 protein / Mdm2-like p53-binding protein / Protein Mdmx / p53-binding protein Mdm4


Mass: 12129.982 Da / Num. of mol.: 1 / Mutation: L46V, V95L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: mdm4, mdmx / Production host: Escherichia coli (E. coli) / References: UniProt: Q7ZUW7
#2: Protein/peptide Stapled peptide QSQQTF(0EH)NLWRLE(MK8)QN(NH2)


Mass: 2087.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100mM Tris-8.0, 2.4M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.25→54.47 Å / Num. obs: 38363 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.565 Å2 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Net I/σ(I): 11.3 / Num. measured all: 248825
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.1 / Num. measured all: 12096 / Num. unique obs: 1894 / Rpim(I) all: 0.7 / Rrim(I) all: 1.783 / % possible all: 99.9

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N5T

4n5t


Resolution: 1.25→54.465 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.74
RfactorNum. reflection% reflection
Rfree0.1962 1909 4.98 %
Rwork0.1694 --
obs0.1707 38348 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.67 Å2 / Biso mean: 26.7134 Å2 / Biso min: 13.56 Å2
Refinement stepCycle: final / Resolution: 1.25→54.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms849 0 5 94 948
Biso mean--92.1 39.55 -
Num. residues----105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005892
X-RAY DIFFRACTIONf_angle_d0.8261209
X-RAY DIFFRACTIONf_dihedral_angle_d2.6707
X-RAY DIFFRACTIONf_chiral_restr0.082132
X-RAY DIFFRACTIONf_plane_restr0.005156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.25-1.28130.3831450.31352583100
1.2813-1.31590.33371410.30182535100
1.3159-1.35470.3031190.26532619100
1.3547-1.39840.30121460.2507254099
1.3984-1.44840.21951310.218251298
1.4484-1.50640.21321390.1857258199
1.5064-1.57490.22541330.1772589100
1.5749-1.6580.20011410.16242605100
1.658-1.76180.18431280.13532602100
1.7618-1.89790.17021390.13672597100
1.8979-2.08890.19311180.143264099
2.0889-2.39110.14821220.14562650100
2.3911-3.01260.21611420.1751263299
3.0126-54.4650.18251650.1704275499

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