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- PDB-8hdg: Small peptide enhances the binding of nutline-3a to MdmX -

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Basic information

Entry
Database: PDB / ID: 8hdg
TitleSmall peptide enhances the binding of nutline-3a to MdmX
ComponentsUncharacterized protein DKFZp686B01123
KeywordsONCOPROTEIN / MdmX / p53 / Nutlin-3a / Enhancement
Function / homologycellular component organization / MDM4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Chem-NUT / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / Uncharacterized protein DKFZp686B01123
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsCheng, X.Y. / Huang, Y. / Wei, Q.Y. / Huang, J.J. / Peng, Y.W. / Su, Z.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Small peptide enhances the binding of nutline-3a to MdmX
Authors: Cheng, X.Y. / Huang, Y. / Wei, Q.Y. / Huang, J.J. / Peng, Y.W. / Su, Z.D.
History
DepositionNov 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Uncharacterized protein DKFZp686B01123
A: Uncharacterized protein DKFZp686B01123
C: Uncharacterized protein DKFZp686B01123
B: Uncharacterized protein DKFZp686B01123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,32212
Polymers50,9384
Non-polymers3,3838
Water2,000111
1
D: Uncharacterized protein DKFZp686B01123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5803
Polymers12,7351
Non-polymers8462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein DKFZp686B01123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5803
Polymers12,7351
Non-polymers8462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uncharacterized protein DKFZp686B01123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3162
Polymers12,7351
Non-polymers5811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Uncharacterized protein DKFZp686B01123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8454
Polymers12,7351
Non-polymers1,1103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.844, 47.879, 92.233
Angle α, β, γ (deg.)90.000, 90.053, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21D
32D
42D
53D
63D
74D
84D
95D
105D
116D
126D

NCS domain segments:

Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Auth asym-ID: D / Label asym-ID: A / Auth seq-ID: 12 - 109 / Label seq-ID: 12 - 109

Dom-IDComponent-IDEns-ID
111
211
322
422
533
633
744
844
955
1055
1166
1266

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein
Uncharacterized protein DKFZp686B01123


Mass: 12734.615 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686B01123 / Production host: Escherichia (bacteria) / References: UniProt: Q6MZR7
#2: Chemical
ChemComp-NUT / 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one / Nutlin 3a


Mass: 581.490 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H30Cl2N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / 18-Crown-6


Mass: 264.315 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H24O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% v/v Tacsimate pH7.0, 0.1 M HEPES pH7.5, 2% v/v Polythylene glycol 200
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.68→47.844 Å / Num. obs: 43877 / % possible obs: 100 % / Redundancy: 23.7 % / CC1/2: 1 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.019 / Rrim(I) all: 0.094 / Net I/σ(I): 25.4
Reflection shellResolution: 1.68→1.71 Å / % possible obs: 99.8 % / Redundancy: 19.9 % / Rmerge(I) obs: 1.256 / Num. measured all: 12710 / Num. unique obs: 639 / CC1/2: 0.84 / Rpim(I) all: 0.287 / Rrim(I) all: 1.289 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMACREFMAC5refinement
xia2data reduction
Aimlessdata scaling
HKL-3000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C3Y

7c3y


Resolution: 1.73→47.844 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.727 / SU ML: 0.087 / Cross valid method: NONE / ESU R: 0.128 / ESU R Free: 0.123
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.241 2302 5.246 %
Rwork0.2045 41575 -
all0.206 --
obs-43877 99.952 %
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: 26.721 Å2
Baniso -1Baniso -2Baniso -3
1-0.386 Å20 Å2-0.07 Å2
2--0.403 Å20 Å2
3----0.789 Å2
Refinement stepCycle: LAST / Resolution: 1.73→47.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 0 232 111 3483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123448
X-RAY DIFFRACTIONr_bond_other_d0.0080.0163201
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.6564635
X-RAY DIFFRACTIONr_angle_other_deg0.5141.5597475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2935388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.9528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79310598
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.15210151
X-RAY DIFFRACTIONr_chiral_restr0.0780.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02636
X-RAY DIFFRACTIONr_nbd_refined0.2480.2717
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22751
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21651
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21782
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.283
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2890.223
X-RAY DIFFRACTIONr_nbd_other0.2270.2141
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.214
X-RAY DIFFRACTIONr_mcbond_it2.7312.4741568
X-RAY DIFFRACTIONr_mcbond_other2.7162.4691564
X-RAY DIFFRACTIONr_mcangle_it4.1063.6791948
X-RAY DIFFRACTIONr_mcangle_other4.1053.6821949
X-RAY DIFFRACTIONr_scbond_it3.8253.0641880
X-RAY DIFFRACTIONr_scbond_other3.8243.0641881
X-RAY DIFFRACTIONr_scangle_it6.074.4192687
X-RAY DIFFRACTIONr_scangle_other6.0694.4192688
X-RAY DIFFRACTIONr_lrange_it8.49438.5743808
X-RAY DIFFRACTIONr_lrange_other8.49938.2123796
X-RAY DIFFRACTIONr_ncsr_local_group_10.070.053046
X-RAY DIFFRACTIONr_ncsr_local_group_20.0750.052977
X-RAY DIFFRACTIONr_ncsr_local_group_30.0770.053027
X-RAY DIFFRACTIONr_ncsr_local_group_40.0850.052966
X-RAY DIFFRACTIONr_ncsr_local_group_50.0870.053014
X-RAY DIFFRACTIONr_ncsr_local_group_60.0890.052964
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11DX-RAY DIFFRACTIONLocal ncs0.07050.0501
12DX-RAY DIFFRACTIONLocal ncs0.07050.0501
23DX-RAY DIFFRACTIONLocal ncs0.074580.0501
24DX-RAY DIFFRACTIONLocal ncs0.074580.0501
35DX-RAY DIFFRACTIONLocal ncs0.076910.0501
36DX-RAY DIFFRACTIONLocal ncs0.076910.0501
47DX-RAY DIFFRACTIONLocal ncs0.084610.0501
48DX-RAY DIFFRACTIONLocal ncs0.084610.0501
59DX-RAY DIFFRACTIONLocal ncs0.086720.0501
510DX-RAY DIFFRACTIONLocal ncs0.086720.0501
611DX-RAY DIFFRACTIONLocal ncs0.089270.0501
612DX-RAY DIFFRACTIONLocal ncs0.089270.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.7750.2841460.2733050X-RAY DIFFRACTION99.9375
1.775-1.8230.3211650.2612980X-RAY DIFFRACTION99.9047
1.823-1.8760.3461120.2582954X-RAY DIFFRACTION99.9674
1.876-1.9340.275970.2242851X-RAY DIFFRACTION99.9661
1.934-1.9970.2821850.2092717X-RAY DIFFRACTION99.9656
1.997-2.0670.311420.2192603X-RAY DIFFRACTION99.9636
2.067-2.1450.2121820.1942511X-RAY DIFFRACTION100
2.145-2.2320.2531920.2032381X-RAY DIFFRACTION100
2.232-2.3310.2071270.1952399X-RAY DIFFRACTION100
2.331-2.4450.2671350.2162218X-RAY DIFFRACTION100
2.445-2.5770.2881510.2022103X-RAY DIFFRACTION100
2.577-2.7330.2671070.2062054X-RAY DIFFRACTION100
2.733-2.9210.2371170.2091881X-RAY DIFFRACTION100
2.921-3.1540.288840.2051849X-RAY DIFFRACTION100
3.154-3.4530.205750.1921642X-RAY DIFFRACTION100
3.453-3.8580.165610.1651507X-RAY DIFFRACTION99.8726
3.858-4.450.182820.1691335X-RAY DIFFRACTION100
4.45-5.4390.189650.181130X-RAY DIFFRACTION99.8329
5.439-7.6420.375510.241869X-RAY DIFFRACTION99.675
7.642-47.8440.199250.216528X-RAY DIFFRACTION99.6396

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