Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

6HUY

HmdII from Desulfurobacterium thermolithotrophum reconstitued with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydrofolate form A

Experimental procedure
Experimental methodSINGLE WAVELENGTH
Source typeSYNCHROTRON
Source detailsSLS BEAMLINE X10SA
Synchrotron siteSLS
BeamlineX10SA
Temperature [K]100
Detector technologyPIXEL
Collection date2018-04-15
DetectorDECTRIS PILATUS 6M
Wavelength(s)1.00000
Spacegroup nameP 21 21 21
Unit cell lengths99.769, 131.829, 168.263
Unit cell angles90.00, 90.00, 90.00
Refinement procedure
Resolution24.983 - 2.250
R-factor0.1881
Rwork0.187
R-free0.21220
Structure solution methodMOLECULAR REPLACEMENT
Starting model (for MR)4yt4
RMSD bond length0.007
RMSD bond angle0.879
Data reduction softwareXDS
Data scaling softwareSCALA (3.3.22)
Phasing softwarePHASER (2.6.0)
Refinement softwarePHENIX ((1.10.1_2155: ???))
Data quality characteristics
 OverallOuter shell
Low resolution limit [Å]48.8902.370
High resolution limit [Å]2.2502.250
Rmerge0.0961.421
Rmeas0.1081.595
Rpim0.0490.714
Number of reflections10563015270
<I/σ(I)>9.7
Completeness [%]99.9100
Redundancy4.84.9
CC(1/2)0.9980.623
Crystallization Conditions
crystal IDmethodpHtemperaturedetails
1VAPOR DIFFUSION, SITTING DROP5.5281dHmdII reconstituted with the Fe-guanylylpyridinol cofactor from Methanothermobacter marburgensis was cocrystallized with methenyl-tetrahydrofolate using the sitting drop vapor diffusion method at 281 K under N2/H2 (95%/5%) in red light condition. The reconstituted dHmdII holoenzyme was mixed with methenyl-tetrahydrofolate at the final concentrations of 1.6 mM. Methenyl-tetrahydrofolate was dissolved in 10% DMSO, and the final concentration of DMSO in the protein solution was 1.6%. 0.7 ul of dHmdII at 21 mg/ml (with Fe-guanylylpryridinol and methenyl-tetrahydrofolate) was spotted on a 96-well 2-drop MRC Crystallization Plates (Molecular Dimensions, Suffolk, UK) and 0.7 ul of reservoir solution was mixed. After 10 days, the crystals appeared in 20% PEG 3000 (w/v), 100 mM Tri-Sodium Citrate pH 5.5 (from the kit Wizard, Jean Bioscience). Crystals were cryoprotected by a soak of few seconds in 20% PEG 3000 (w/v), 100 mM Tri-Sodium Citrate pH 5.5 and 20% glycerol before a flash freeze in liquid nitrogen.

217705

PDB entries from 2024-03-27

PDB statisticsPDBj update infoContact PDBjnumon