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- PDB-4rxz: Crystal Structure of MDMX phosporylated Tyr99 in complex with a 1... -

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Basic information

Entry
Database: PDB / ID: 4rxz
TitleCrystal Structure of MDMX phosporylated Tyr99 in complex with a 12-mer peptide
Components
  • 12-MER PEPTIDE INHIBITOR
  • Protein Mdm4
KeywordsINHIBITOR / MDM4 / MDMX-PEPTIDE INHIBITOR COMPLEX / ONCOPROTEIN / METAL-BINDING / PMI
Function / homology
Function and homology information


atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process ...atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process / Regulation of TP53 Activity through Methylation / ubiquitin-protein transferase activity / Regulation of TP53 Degradation / cellular response to hypoxia / protein-containing complex assembly / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / protein stabilization / protein ubiquitination / regulation of cell cycle / Ub-specific processing proteases / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / enzyme binding / zinc ion binding / nucleoplasm / nucleus
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 / Zn-finger in Ran binding protein and others / Zinc finger, C3HC4 type (RING finger) ...MDM4 / MDM2 / SWIB/MDM2 domain / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others / 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-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPazgier, M. / Gohain, N. / Tolbert, W.D.
CitationJournal: Oncogene / Year: 2016
Title: Structural basis of how stress-induced MDMX phosphorylation activates p53.
Authors: Chen, X. / Gohain, N. / Zhan, C. / Lu, W.Y. / Pazgier, M. / Lu, W.
History
DepositionDec 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations / Category: citation / database_2 / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Mdm4
C: 12-MER PEPTIDE INHIBITOR
B: Protein Mdm4
D: 12-MER PEPTIDE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)22,5104
Polymers22,5104
Non-polymers00
Water2,540141
1
A: Protein Mdm4
C: 12-MER PEPTIDE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)11,2552
Polymers11,2552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-12 kcal/mol
Surface area5670 Å2
MethodPISA
2
B: Protein Mdm4
D: 12-MER PEPTIDE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)11,2552
Polymers11,2552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-13 kcal/mol
Surface area5520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.613, 41.430, 45.618
Angle α, β, γ (deg.)103.32, 103.67, 102.44
Int Tables number1
Space group name H-MP1

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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: 9827.411 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthesized based on the human MDMX sequence residues 24-108 and Tyrosine at position 99 is phosphorylated
Source: (synth.) Homo sapiens (human) / References: UniProt: O15151
#2: Protein/peptide 12-MER PEPTIDE INHIBITOR


Mass: 1427.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 12-mer peptide inhibitor based on human p53
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% isopropanol, 0.1M MES pH 6.5 and 10% PEG5000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9753 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 4, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9753 Å / Relative weight: 1
ReflectionResolution: 1.55→42.33 Å / Num. all: 27683 / Num. obs: 25745 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.14
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 1.1 / Num. unique all: 1545 / % possible all: 87.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EQY

3eqy


Resolution: 1.55→42.33 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.206 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22034 1341 5.1 %RANDOM
Rwork0.18044 ---
all0.18249 26342 --
obs0.18249 24762 94.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.003 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0.54 Å20.46 Å2
2---0.16 Å20.22 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.55→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 0 141 1655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191546
X-RAY DIFFRACTIONr_bond_other_d0.0010.021510
X-RAY DIFFRACTIONr_angle_refined_deg1.9642.0032090
X-RAY DIFFRACTIONr_angle_other_deg0.9933468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4585185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97124.37564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5615273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.265156
X-RAY DIFFRACTIONr_chiral_restr0.1390.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211707
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02351
X-RAY DIFFRACTIONr_mcbond_it2.8282.627752
X-RAY DIFFRACTIONr_mcbond_other2.8132.625751
X-RAY DIFFRACTIONr_mcangle_it3.9883.901933
X-RAY DIFFRACTIONr_mcangle_other3.9953.902934
X-RAY DIFFRACTIONr_scbond_it3.8543.119794
X-RAY DIFFRACTIONr_scbond_other3.8513.119795
X-RAY DIFFRACTIONr_scangle_other5.7674.5381158
X-RAY DIFFRACTIONr_long_range_B_refined7.61122.2971846
X-RAY DIFFRACTIONr_long_range_B_other7.52321.7141785
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 95 -
Rwork0.313 1722 -
obs--87.02 %

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