The CCP4 Study Weekend starts today! Take a look at our most recent virtual issue collecting articles based on presentations at the meeting: tinyurl.com/5n79tuyu
StructuralBiology
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Acta Crystallographica Section D: Structural Biology is a leading structural biology journal published by the IUCr.
"When generating structures from crystallographic data, one should ignore whatever inferences may have been drawn about them using noncrystallographic techniques if possible" #PhotosystemII #LowOxidationParadigm #HighOxidationParadigm https://t.co/VOYEqAgl7D
Photosystem II: light-dependent oscillation of ligand composition at its active site
Analysis of light-dependent changes in the number of oxygen ligands in the CaMn4 cluster of the oxygen-evolving center suggests a possible mechanism for O&z-dbnd;O bond formation by photosystem II.
The 1.3 Å resolution crystal structure of the N-terminally truncated type IV pilin from Pseudomonas aeruginosa strain P1 is the first to be reported from this group @yorkuniversity @IUCr #TypeIVPilins #PseudomonasAeruginosa #AIGeneratedModels https://doi.org/10.1107/S205979832401132X
The 1.3 Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1
The structure of a type IV pilin from a human-pathogenic strain of P. aeruginosa was solved to 1.3 Å resolution using molecular replacement with an AlphaFold-generated search model. It is the first structure from this group of pilins to be discussed and reveals the structural differences that result in functional diversity between closely related type IV pili.
A new program, MetalCoord, is described that classifies and utilizes the metal-coordination geometry and has been used to update metal-containing components from the CCP4 monomer library #Refinement #Restraints #MetalCoordinationGeometry https://t.co/GEAMKSEpTc
Atomic structures of biological molecules have never been so available and ubiquitous, but this raises questions as to how they are made appropriately accessible for optimal use https://t.co/RTx2WLxR0W
Our final issue of 2024 is out: https://tinyurl.com/4efts8bb
The cover shows the refinement of the coordination of a magesium cation in a cryoEM structure of chlorophyll using metal-coordination restraints extracted from the Crystallography Open Database https://tinyurl.com/3w8zrdmf
The behavior of a number of iterative projection algorithms for crystallographic phase retrieval is investigated #AbInitioPhaseDetermination #CrystallographicImaging #IterativeProjectionAlgorithms https://doi.org/10.1107/S2059798324009902
Analysis of crystallographic phase retrieval using iterative projection algorithms
The behavior of iterative projection algorithms for crystallographic phase retrieval is systematically investigated. It is shown that information present in the algorithm trajectory following convergence can be exploited to improve the final density estimate.
The structure, stability and substrate preference of a thermophilic bioplastic-degrading enzyme were determined, with implications for bioplastic degradation in waste management #SerineHydrolases #BioplasticDegradation #ThermalStability https://doi.org/10.1107/S2059798324009707
Structure and stability of an apo thermophilic esterase that hydrolyzes polyhydroxybutyrate
A future involving plastics that can be degraded and resynthesized requires an appropriate plastic to be found, plus green solutions that are compatible with waste-management systems. Here, the structure, stability and substrate-size preference are reported for a recently identified thermophilic serine hydrolase that degrades bioplastics such as polyhydroxybutyrate and other polymers.
EMhub is a web platform designed to support the daily operations and record-keeping of a scientific facility; it was initially developed to meet the needs of the Swedish National CryoEM Facility #DataManagement #WebApplication #ScientificFacilities https://doi.org/10.1107/S2059798324009471
EMhub: a web platform for data management and on-the-fly processing in scientific facilities
This article presents EMhub, a web platform designed to support the daily operations of a scientific facility. EMhub enables the easy management of users, instruments, bookings and project tracking. The application was initially developed to meet the needs of a cryoEM facility, but the versatility of its design makes it suitable for extension to other areas.
How many of the PDB models that were solved using experimental phasing could have been solved by molecular replacement using models obtained from AlphaFold? #MolecularReplacement #AlphaFold2 #ComputationalMethods https://t.co/s6EahtcYms
The success rate of processed predicted models in molecular replacement: implications for experimental phasing in the AlphaFold era
A large set of SAD-phased PDB depositions were tested for solubility by molecular replacement using AlphaFold2 and other approaches. The 3% of cases that were not solved help to show where experimental phasing efforts could be focused in the future.