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- PDB-7o9t: Crystal structure of Human Menin in apo form -

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Basic information

Entry
Database: PDB / ID: 7o9t
TitleCrystal structure of Human Menin in apo form
ComponentsMenin
KeywordsONCOPROTEIN
Function / homologyMenin / Menin / DNA binding / nucleus / Menin
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.159 Å
AuthorsGroves, M.R. / Gao, K.
CitationJournal: To Be Published
Title: Crystal structure of Human Menin in apo form
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)54,9573
Polymers54,8331
Non-polymers1242
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint5 kcal/mol
Surface area19770 Å2
Unit cell
Length a, b, c (Å)107.323, 107.323, 106.729
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-824-

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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.8 Å3/Da / Density % sol: 37.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 12% PEG 3350 14% Glycerol / Temp details: in cold room

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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: 2.159→50 Å / Num. obs: 34097 / % possible obs: 99.94 % / Redundancy: 11.7 % / Biso Wilson estimate: 35.93 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 18.09
Reflection shellResolution: 2.159→2.236 Å / Redundancy: 12 % / Rmerge(I) obs: 0.4779 / Mean I/σ(I) obs: 4.27 / Num. unique obs: 3342 / CC1/2: 0.949 / CC star: 0.987 / Rpim(I) all: 0.142 / Rrim(I) all: 0.4989 / % 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: 2.159→47.996 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 1580 4.63 %
Rwork0.2073 32514 -
obs0.2093 34094 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.81 Å2 / Biso mean: 41.6412 Å2 / Biso min: 19.64 Å2
Refinement stepCycle: final / Resolution: 2.159→47.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 8 95 3717
Biso mean--43.37 37.59 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073698
X-RAY DIFFRACTIONf_angle_d0.8285007
X-RAY DIFFRACTIONf_chiral_restr0.047559
X-RAY DIFFRACTIONf_plane_restr0.005639
X-RAY DIFFRACTIONf_dihedral_angle_d9.7882198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.159-2.22870.3251510.25032881
2.2287-2.30830.31061290.24382908
2.236-4.80010.23781290.19163209
2.3083-2.40080.26531860.23212858
2.4008-2.510.33871430.23482915
2.51-2.64230.28421360.22872918
2.6423-2.80790.30571740.24032906
2.8079-3.02460.24161300.21712946
3.0246-3.3290.24021180.21012981
3.329-3.81050.22251390.19862989
3.8105-4.80010.22241450.18423003

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