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- PDB-7ahy: Crystal structure of Western clawed frog MDM2 RING domain homodimer -

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Basic information

Entry
Database: PDB / ID: 7ahy
TitleCrystal structure of Western clawed frog MDM2 RING domain homodimer
ComponentsE3 ubiquitin-protein ligase Mdm2
KeywordsLIGASE / Ubiquitin ligase / RING E3
Function / homology
Function and homology information


regulation of biological quality / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / regulation of cell cycle / nucleolus / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Ubiquitin-protein ligase E3 MDM2 / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / 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 RanBP2 type profile. ...Ubiquitin-protein ligase E3 MDM2 / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / 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 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
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesXenopus tropicalis (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.532 Å
AuthorsMagnussen, H.M. / Huang, D.T.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKA17196 United Kingdom
Cancer Research UKA29256 United Kingdom
European Research Council (ERC)647849 United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Identification of a Catalytic Active but Non-Aggregating MDM2 RING Domain Variant.
Authors: Magnussen, H.M. / Huang, D.T.
History
DepositionSep 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 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.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 10, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: E3 ubiquitin-protein ligase Mdm2
BBB: E3 ubiquitin-protein ligase Mdm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0786
Polymers15,8172
Non-polymers2624
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-13 kcal/mol
Surface area6190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.559, 23.760, 55.744
Angle α, β, γ (deg.)90.000, 101.224, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains A B)

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Components

#1: Protein E3 ubiquitin-protein ligase Mdm2


Mass: 7908.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: G412, S413: Expression tag
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: mdm2, irak1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6P3Q9, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M PCTP, 25 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97997 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97997 Å / Relative weight: 1
ReflectionResolution: 2.53→41.75 Å / Num. obs: 3830 / % possible obs: 99.8 % / Redundancy: 3.1 % / CC1/2: 0.983 / Net I/σ(I): 3.7
Reflection shellResolution: 2.53→2.6 Å / Num. unique obs: 274 / CC1/2: 0.652

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
xia2data reduction
Aimless0.5.32data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AH2

7ah2


Resolution: 2.532→41.745 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.87 / SU B: 15.064 / SU ML: 0.319 / Cross valid method: FREE R-VALUE / ESU R: 0.888 / ESU R Free: 0.343
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2788 198 5.17 %
Rwork0.2167 3632 -
all0.22 --
obs-3830 99.532 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.802 Å2
Baniso -1Baniso -2Baniso -3
1-0.339 Å20 Å20.296 Å2
2--1.592 Å2-0 Å2
3----1.899 Å2
Refinement stepCycle: LAST / Resolution: 2.532→41.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms822 0 4 4 830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.013836
X-RAY DIFFRACTIONr_bond_other_d0.0020.017775
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.6641137
X-RAY DIFFRACTIONr_angle_other_deg1.2261.5741807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.025111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05722.524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.36515132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.219152
X-RAY DIFFRACTIONr_chiral_restr0.0570.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02909
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02145
X-RAY DIFFRACTIONr_nbd_refined0.1830.2147
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.2673
X-RAY DIFFRACTIONr_nbtor_refined0.1510.2391
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2358
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.215
X-RAY DIFFRACTIONr_metal_ion_refined0.0180.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2680.214
X-RAY DIFFRACTIONr_nbd_other0.2270.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.21
X-RAY DIFFRACTIONr_mcbond_it2.5984.703450
X-RAY DIFFRACTIONr_mcbond_other2.5984.698449
X-RAY DIFFRACTIONr_mcangle_it4.1957.045559
X-RAY DIFFRACTIONr_mcangle_other4.1927.05560
X-RAY DIFFRACTIONr_scbond_it2.6094.998386
X-RAY DIFFRACTIONr_scbond_other2.6065.002387
X-RAY DIFFRACTIONr_scangle_it4.227.342578
X-RAY DIFFRACTIONr_scangle_other4.227.342578
X-RAY DIFFRACTIONr_lrange_it6.95156.566839
X-RAY DIFFRACTIONr_lrange_other6.94856.602840
X-RAY DIFFRACTIONr_ncsr_local_group_10.0980.051414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.532-2.5980.335110.3072580.3082790.7770.78596.41580.303
2.598-2.6690.36160.3032570.3062750.7110.75599.27270.309
2.669-2.7460.33780.3062450.3072530.5280.7581000.304
2.746-2.830.273120.2772430.2772550.8570.7821000.282
2.83-2.9220.288120.2812410.2822530.8810.8091000.282
2.922-3.0240.311160.262260.2632420.8320.8341000.256
3.024-3.1380.401140.2322060.242200.70.8661000.231
3.138-3.2650.26780.2132270.2152370.870.8899.15610.21
3.265-3.410.28130.2272000.2312130.9250.8781000.224
3.41-3.5750.308110.2141960.222070.8420.8951000.209
3.575-3.7670.265170.1761860.1852050.9340.92799.02440.177
3.767-3.9930.25970.1991850.2021920.9490.9211000.199
3.993-4.2660.214160.1931560.1951720.9190.9411000.192
4.266-4.6040.28590.1611580.1671670.9160.9561000.167
4.604-5.0370.20970.1571430.1591500.950.9581000.169
5.037-5.6210.16250.1881400.1871460.9330.94899.31510.195
5.621-6.4710.61230.2291200.2361230.7640.921000.236
6.471-7.8790.24440.1911100.1921140.8370.9411000.205
7.879-10.9490.27340.255840.255880.9460.9421000.295
10.949-41.7450.34950.224500.23550.9120.9631000.265

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