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- PDB-6cob: AtHNL enantioselectivity mutant At-A9-H7 Apo, Y13C,Y121L,P126F,L1... -

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Basic information

Entry
Database: PDB / ID: 6cob
TitleAtHNL enantioselectivity mutant At-A9-H7 Apo, Y13C,Y121L,P126F,L128W,C131T,F179L,A209I
ComponentsAlpha-hydroxynitrile lyase
KeywordsLYASE / alpha beta hydrolase globular hydroxynitrile lyase
Function / homology
Function and homology information


mandelonitrile lyase activity / (R)-mandelonitrile lyase / glycoside catabolic process / response to wounding
Similarity search - Function
Methylesterase/Alpha-hydroxynitrile lyase / Alpha/beta hydrolase family / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-hydroxynitrile lyase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 Å
AuthorsJones, B.J. / Kazlauskas, R.J. / Desrouleaux, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM102205 United States
CitationJournal: To be published
Title: AtHNL enantioselectivity mutants
Authors: Jones, B.J. / Desrouleaux, R. / Kazlauskas, R.J.
History
DepositionMar 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-hydroxynitrile lyase
B: Alpha-hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2337
Polymers58,8862
Non-polymers3475
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-44 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.982, 87.110, 123.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha-hydroxynitrile lyase / AtHNL / (R)-hydroxynitrile lyase / (R)-oxynitrilase / Methylesterase 5 / AtMES5


Mass: 29442.980 Da / Num. of mol.: 2 / Fragment: AtHNL / Mutation: Y13C,Y121L,P126F,L128W,C131T,F179L,A209I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HNL, MES5, At5g10300, F18D22_70 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LFT6, (R)-mandelonitrile lyase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.29 Å3/Da / Density % sol: 46.37 % / Mosaicity: 0.378 ° / Mosaicity esd: 0.006 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1 M bis-tris, 17% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2016
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 48970 / % possible obs: 99.9 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.042 / Rrim(I) all: 0.117 / Χ2: 0.974 / Net I/σ(I): 5.7 / Num. measured all: 387194
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.82-1.857.70.98524250.7340.3740.84499.8
1.85-1.897.90.86123950.7570.3230.85399.90.921
1.89-1.927.90.76724180.8170.2870.88199.90.82
1.92-1.967.90.65823960.8620.2460.881000.704
1.96-27.70.56224330.8810.2130.9311000.602
2-2.057.20.45423990.9060.180.9511000.49
2.05-2.180.39924210.9340.1480.97199.90.427
2.1-2.168.20.32924070.960.120.99599.90.351
2.16-2.228.20.27624330.9690.1011.0261000.294
2.22-2.298.10.23724470.9780.0881.00599.90.253
2.29-2.3780.20124360.9790.0750.9691000.214
2.37-2.477.50.17324250.9830.0671.03599.80.186
2.47-2.5880.14724240.9870.0551.00999.90.157
2.58-2.728.30.13424430.9910.0491.0091000.143
2.72-2.898.20.11424580.9930.0421.02599.90.122
2.89-3.1180.09524690.9950.0351.00599.80.102
3.11-3.437.70.07924610.9950.031.0221000.085
3.43-3.928.30.06624900.9970.0241.0341000.071
3.92-4.947.60.05325250.9980.021.01399.60.057
4.94-507.70.04826650.9980.0181.00999.70.052

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.29 Å43.35 Å
Translation7.29 Å43.35 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0155refinement
DENZOdata reduction
HKL-2000data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3DQZ

3dqz


Resolution: 1.82→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.129 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.108
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1867 2375 4.9 %RANDOM
Rwork0.1516 ---
obs0.1533 46522 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.64 Å2 / Biso mean: 27.272 Å2 / Biso min: 11.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 1.82→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 20 245 4373
Biso mean--44.78 32.28 -
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0194366
X-RAY DIFFRACTIONr_bond_other_d0.0020.024156
X-RAY DIFFRACTIONr_angle_refined_deg2.4431.9635914
X-RAY DIFFRACTIONr_angle_other_deg1.22639627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4115544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51524.167192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83115785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1981520
X-RAY DIFFRACTIONr_chiral_restr0.1640.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214910
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02982
LS refinement shellResolution: 1.821→1.869 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 173 -
Rwork0.231 3342 -
all-3515 -
obs--97.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2344-0.0359-0.03130.73130.30120.9833-0.0656-0.2365-0.08710.12940.00160.03520.0869-0.06970.0640.02730.00940.01280.05480.01290.0116-33.01052.6807-3.0914
21.2544-0.162-0.14530.6533-0.0340.51870.00810.15370.0269-0.08140.004-0.0653-0.0040.0239-0.01210.0191-0.00130.01720.0347-0.01380.0374-15.62787.0764-33.1264
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 258
2X-RAY DIFFRACTION2B1 - 258

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