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- PDB-8euo: Hydroxynitrile Lyase from Hevea brasiliensis with Seven Mutations -

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Basic information

Entry
Database: PDB / ID: 8euo
TitleHydroxynitrile Lyase from Hevea brasiliensis with Seven Mutations
Components(S)-hydroxynitrile lyase
KeywordsLYASE / Engineered Protein / alpha/beta hydrolase fold / esterase / catalytic promiscuity
Function / homology
Function and homology information


(S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity / jasmonic acid metabolic process / methyl salicylate esterase activity / methyl jasmonate esterase activity / salicylic acid metabolic process / methyl indole-3-acetate esterase activity
Similarity search - Function
Methylesterase/Alpha-hydroxynitrile lyase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
(S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsGreenberg, L.R. / Walsh, M.E. / Kazlauskas, R.J. / Pierce, C.T. / Shi, K. / Aihara, H. / Evans, R.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119483 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIGMS R35-GM118047 United States
National Science Foundation (NSF, United States)2039039 United States
Citation
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: 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
DepositionOct 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: 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: (S)-hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)30,2591
Polymers30,2591
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10030 Å2
Unit cell
Length a, b, c (Å)47.054, 106.378, 128.396
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein (S)-hydroxynitrile lyase / (S)-acetone-cyanohydrin lyase / Oxynitrilase


Mass: 30258.736 Da / Num. of mol.: 1 / Mutation: T11G, E79H, C81L, H103V, N104A, G176S, K236M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Gene: HNL / Production host: Escherichia coli (E. coli) / References: UniProt: P52704, (S)-hydroxynitrile lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.67 % / Description: elongated trapezoid
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M BIS TRIS, 2.0 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→43.03 Å / Num. obs: 20181 / % possible obs: 89.43 % / Redundancy: 5.1 % / Biso Wilson estimate: 28.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.032 / Rrim(I) all: 0.077 / Rsym value: 0.063 / Net I/σ(I): 13.9
Reflection shellResolution: 1.99→2.04 Å / Rmerge(I) obs: 0.748 / Num. unique obs: 1606 / CC1/2: 0.689 / Rpim(I) all: 0.828 / Rrim(I) all: 0.347 / Rsym value: 0.748 / % possible all: 89.95

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000721.3data reduction
HKL-2000721.3data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C6X

3c6x


Resolution: 1.99→43.03 Å / SU ML: 0.2296 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.0388
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2376 2000 9.91 %
Rwork0.1844 18181 -
obs0.1896 20181 89.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.63 Å2
Refinement stepCycle: LAST / Resolution: 1.99→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 0 132 2137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842090
X-RAY DIFFRACTIONf_angle_d1.02762851
X-RAY DIFFRACTIONf_chiral_restr0.06320
X-RAY DIFFRACTIONf_plane_restr0.0079359
X-RAY DIFFRACTIONf_dihedral_angle_d6.7181281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.25581360.23091229X-RAY DIFFRACTION85.31
2.04-2.090.27731500.21451375X-RAY DIFFRACTION96.95
2.09-2.160.27451550.21551402X-RAY DIFFRACTION96.89
2.16-2.230.27121510.18881375X-RAY DIFFRACTION95.97
2.23-2.310.24311480.19151347X-RAY DIFFRACTION94.8
2.31-2.40.27881480.19851347X-RAY DIFFRACTION93.73
2.4-2.510.31191490.20881346X-RAY DIFFRACTION93.55
2.51-2.640.24441450.20321326X-RAY DIFFRACTION91.2
2.64-2.80.28151400.2131271X-RAY DIFFRACTION88.63
2.8-3.020.25031400.21111272X-RAY DIFFRACTION87.92
3.02-3.320.27121380.20791253X-RAY DIFFRACTION85.86
3.32-3.80.21881290.17231179X-RAY DIFFRACTION79.95
3.81-4.790.16771260.13711143X-RAY DIFFRACTION77.19
4.79-43.030.20631450.1581316X-RAY DIFFRACTION84.4

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