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- PDB-7o9x: Crystal structure of Human Menin with fragment 16 -

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Basic information

Entry
Database: PDB / ID: 7o9x
TitleCrystal structure of Human Menin with fragment 16
ComponentsMenin
KeywordsONCOPROTEIN
Function / homologyMenin / Menin / DNA binding / nucleus / (2-methoxyphenyl)methanamine / Menin
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å
AuthorsGroves, M.R. / Gao, K.
CitationJournal: To Be Published
Title: Crystal structure of Human Menin with fragment 16
Authors: Groves, M.R. / Gao, K.
History
DepositionApr 17, 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)55,3417
Polymers54,8331
Non-polymers5086
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint8 kcal/mol
Surface area19650 Å2
Unit cell
Length a, b, c (Å)107.063, 107.063, 107.243
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-710-

HOH

21A-770-

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-V6Q / (2-methoxyphenyl)methanamine


Mass: 137.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.8 Å3/Da / Density % sol: 56.11 %
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: 2.299→50 Å / Num. obs: 28344 / % possible obs: 99.88 % / Redundancy: 10.9 % / Biso Wilson estimate: 41.55 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1235 / Rpim(I) all: 0.03953 / Rrim(I) all: 0.1299 / Net I/σ(I): 12.4
Reflection shellResolution: 2.299→2.381 Å / Num. unique obs: 2761 / CC1/2: 0.953 / CC star: 0.988 / % possible all: 99.42

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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: 2.299→47.944 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 1310 4.62 %
Rwork0.1983 27025 -
obs0.2006 28335 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.36 Å2 / Biso mean: 48.5905 Å2 / Biso min: 20.35 Å2
Refinement stepCycle: final / Resolution: 2.299→47.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3611 0 34 145 3790
Biso mean--51.66 46.46 -
Num. residues----458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073718
X-RAY DIFFRACTIONf_angle_d0.8615028
X-RAY DIFFRACTIONf_chiral_restr0.05558
X-RAY DIFFRACTIONf_plane_restr0.005641
X-RAY DIFFRACTIONf_dihedral_angle_d11.2812205
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.299-2.39110.27871760.238288799
2.3911-2.49990.31191510.23152936100
2.4999-2.63170.30261420.22912960100
2.6317-2.79650.31031730.23162931100
2.7965-3.01240.26521270.21672987100
3.0124-3.31550.25691220.19963021100
3.3155-3.79510.23931450.19273013100
3.7951-4.78080.20311420.1723047100
4.7808-50.24271320.19283243100

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