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- PDB-7o9z: Crystal structure of Human Menin in complex with BD-08 -

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Basic information

Entry
Database: PDB / ID: 7o9z
TitleCrystal structure of Human Menin in complex with BD-08
ComponentsMenin
KeywordsONCOPROTEIN
Function / homologyMenin / Menin / DNA binding / nucleus / Chem-V6N / Menin
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.979 Å
AuthorsGroves, M.R. / Gao, K.
CitationJournal: To Be Published
Title: Crystal structure of Human Menin in complex with BD-08
Authors: Groves, M.R. / Gao, K.
History
DepositionApr 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Menin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5297
Polymers54,8331
Non-polymers6966
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint7 kcal/mol
Surface area20000 Å2
Unit cell
Length a, b, c (Å)107.193, 107.193, 107.443
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-729-

HOH

21A-865-

HOH

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Components

#1: Protein Menin


Mass: 54833.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEN1, hCG_2017452 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A024R5E3
#2: Chemical ChemComp-V6N / (~{E})-2-cyano-3-(2~{H}-indazol-6-yl)-~{N}-(2-morpholin-4-ylethyl)prop-2-enamide


Mass: 325.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 12% PEG 3350 14% Glycerol / PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.979→48.03 Å / Num. obs: 44239 / % possible obs: 99.94 % / Redundancy: 11.7 % / Biso Wilson estimate: 35.19 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.08 / Net I/σ(I): 19.08
Reflection shellResolution: 1.979→2.05 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.5146 / Mean I/σ(I) obs: 3.62 / Num. unique obs: 4358 / CC1/2: 0.942 / CC star: 0.985 / Rrim(I) all: 0.5384 / % possible all: 99.73

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DDC

5ddc


Resolution: 1.979→48.028 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2435 2392 5.41 %
Rwork0.2112 41844 -
obs0.2129 44236 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.7 Å2 / Biso mean: 45.9728 Å2 / Biso min: 17.01 Å2
Refinement stepCycle: final / Resolution: 1.979→48.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3635 0 48 187 3870
Biso mean--56.1 42.66 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013765
X-RAY DIFFRACTIONf_angle_d0.955092
X-RAY DIFFRACTIONf_chiral_restr0.059560
X-RAY DIFFRACTIONf_plane_restr0.006651
X-RAY DIFFRACTIONf_dihedral_angle_d10.0973078
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.98-2.01930.31051490.2778241499
2.0193-2.06320.31761550.25262387100
2.0632-2.11120.29321470.24812415100
2.1112-2.1640.29351300.24142424100
2.164-2.22250.25741550.24612412100
2.2225-2.28790.27961590.2492406100
2.2879-2.36170.31291710.2482393100
2.3617-2.44610.32381110.24382495100
2.4461-2.54410.26561550.24172407100
2.5441-2.65990.31451100.23232473100
2.6599-2.80010.25911040.23352480100
2.8001-2.97550.28081430.22262473100
2.9755-3.20520.26371240.2222468100
3.2052-3.52760.2331310.20632492100
3.5276-4.03790.21161670.18862476100
4.0379-5.08640.19021270.17992561100
5.0864-100.21061540.18812668100

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