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- PDB-3fea: Crystal Structure of HdmX bound to the p53-peptidomimetic Ac-Phe-... -

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Entry
Database: PDB / ID: 3fea
TitleCrystal Structure of HdmX bound to the p53-peptidomimetic Ac-Phe-Met-Aib-Pmp-6-Cl-Trp-Glu-Ac3c-Leu-NH2 at 1.33A
Components
  • Mdm4 protein
  • p53-peptidomimetic Ac-Phe-Met-Aib-Pmp-6-Cl-Trp-Glu-Ac3c-Leu-NH2
KeywordsCELL CYCLE / HdmX / Hdm4 / human Mdm4 / human MdmX / protein-protein interaction / p53 / Metal-binding / Nucleus / Polymorphism / Zinc / Zinc-finger
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 / Ub-specific processing proteases / regulation of cell cycle / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / 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: 1.33 Å
AuthorsKallen, J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal Structures of Human MdmX (HdmX) in Complex with p53 Peptide Analogues Reveal Surprising Conformational Changes
Authors: Kallen, J. / Goepfert, A. / Blechschmidt, A. / Izaac, A. / Geiser, M. / Tavares, G. / Ramage, P. / Furet, P. / Masuya, K. / Lisztwan, J.
History
DepositionNov 28, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 22, 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

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Assembly

Deposited unit
A: Mdm4 protein
L: p53-peptidomimetic Ac-Phe-Met-Aib-Pmp-6-Cl-Trp-Glu-Ac3c-Leu-NH2
M: p53-peptidomimetic Ac-Phe-Met-Aib-Pmp-6-Cl-Trp-Glu-Ac3c-Leu-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6914
Polymers13,5723
Non-polymers1181
Water1,47782
1
A: Mdm4 protein
L: p53-peptidomimetic Ac-Phe-Met-Aib-Pmp-6-Cl-Trp-Glu-Ac3c-Leu-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4983
Polymers12,3802
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-29 kcal/mol
Surface area5550 Å2
MethodPISA
2
M: p53-peptidomimetic Ac-Phe-Met-Aib-Pmp-6-Cl-Trp-Glu-Ac3c-Leu-NH2


  • defined by author&software
  • 1.19 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1931
Polymers1,1931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.249, 42.249, 70.449
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 11186.985 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 14-111 / Mutation: C17S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM4, MDMX / Plasmid: pET28 derivative pXI607e / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15151
#2: Protein/peptide p53-peptidomimetic Ac-Phe-Met-Aib-Pmp-6-Cl-Trp-Glu-Ac3c-Leu-NH2


Mass: 1192.731 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Peptide synthesis
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.32 Å3/Da / Density % sol: 46.9 % / Mosaicity: 0.604 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 3.1M AmSo4, 1% MPD, 0.1M MES, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98371 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98371 Å / Relative weight: 1
ReflectionResolution: 1.33→20 Å / Num. obs: 27490 / % possible obs: 97.1 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.062 / Χ2: 1.036 / Net I/σ(I): 39.165
Reflection shellResolution: 1.33→1.38 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.266 / Num. unique all: 2078 / Χ2: 0.118 / % possible all: 74.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
REFMAC5.5.0039phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FE7

3fe7


Resolution: 1.33→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.207 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.872 / SU B: 0.83 / SU ML: 0.035 / SU R Cruickshank DPI: 0.054 / SU Rfree: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1388 5.1 %RANDOM
Rwork0.193 ---
obs0.194 27453 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.73 Å2 / Biso mean: 21.503 Å2 / Biso min: 8.79 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.33→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 0 90 930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021868
X-RAY DIFFRACTIONr_angle_refined_deg1.5842.2221179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.453582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.67524.66730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.67415130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.456153
X-RAY DIFFRACTIONr_chiral_restr0.0930.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021647
X-RAY DIFFRACTIONr_mcbond_it1.0071.5411
X-RAY DIFFRACTIONr_mcangle_it1.8942660
X-RAY DIFFRACTIONr_scbond_it2.6443457
X-RAY DIFFRACTIONr_scangle_it4.1544.5513
LS refinement shellResolution: 1.33→1.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 74 -
Rwork0.291 1297 -
all-1371 -
obs--65.22 %

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