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- PDB-9azb: Crystal structure of LolTv5 -

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Basic information

Entry
Database: PDB / ID: 9azb
TitleCrystal structure of LolTv5
ComponentsAminotransferase, class V/Cysteine desulfurase
KeywordsBIOSYNTHETIC PROTEIN / Mannichase
Function / homologyAminotransferase class V domain / Aminotransferase class-V / transaminase activity / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / PYRIDOXAL-5'-PHOSPHATE / Aminotransferase, class V/Cysteine desulfurase
Function and homology information
Biological speciesPenicillium expansum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGao, J. / Hai, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM151205 United States
Citation
Journal: To Be Published
Title: Enzymatic synthesis of unprotected alpha,beta-diamino acids via direct asymmetric Mannich reactions
Authors: Gao, J. / Hai, Y.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase, class V/Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2042
Polymers52,9561
Non-polymers2471
Water00
1
A: Aminotransferase, class V/Cysteine desulfurase
hetero molecules

A: Aminotransferase, class V/Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4074
Polymers105,9132
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area6860 Å2
ΔGint-43 kcal/mol
Surface area29350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.530, 77.530, 150.685
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Aminotransferase, class V/Cysteine desulfurase


Mass: 52956.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium expansum (fungus) / Gene: PEX2_110450 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A2J6G6
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MES buffer, pH=5.8, 18%PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 R 1M / Detector: PIXEL / Date: Mar 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.9→37.54 Å / Num. obs: 12161 / % possible obs: 99.8 % / Redundancy: 17.5 % / Biso Wilson estimate: 78.55 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.044 / Net I/σ(I): 29.5
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 16.1 % / Rmerge(I) obs: 1.545 / Num. unique obs: 6103 / CC1/2: 0.856 / Rpim(I) all: 0.391 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→37.54 Å / SU ML: 0.4527 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 41.1628
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3423 636 5.25 %
Rwork0.2836 11468 -
obs0.287 12104 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.39 Å2
Refinement stepCycle: LAST / Resolution: 2.9→37.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 0 0 3163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063240
X-RAY DIFFRACTIONf_angle_d0.86954406
X-RAY DIFFRACTIONf_chiral_restr0.0493491
X-RAY DIFFRACTIONf_plane_restr0.007566
X-RAY DIFFRACTIONf_dihedral_angle_d16.2321181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.120.3954960.38852265X-RAY DIFFRACTION98.99
3.13-3.440.47861160.33142264X-RAY DIFFRACTION99.71
3.44-3.940.3761310.31672271X-RAY DIFFRACTION99.75
3.94-4.950.33811250.2892295X-RAY DIFFRACTION99.92
4.96-37.540.3061680.23542373X-RAY DIFFRACTION99.37

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