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

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Basic information

Entry
Database: PDB / ID: 6coc
TitleAtHNL enantioselectivity mutant At-A9-H7 Apo, Y13C,Y121L,P126F,L128W,C131T,F179L,A209I with benzaldehyde
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
benzaldehyde / Alpha-hydroxynitrile lyase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 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 1.2Jan 1, 2020Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,87013
Polymers58,8862
Non-polymers98411
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-45 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.560, 86.720, 122.030
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-HBX / benzaldehyde


Mass: 106.122 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H6O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.23 Å3/Da / Density % sol: 44.76 % / Mosaicity: 0.355 ° / Mosaicity esd: 0.006 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 / 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: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 40386 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.039 / Rrim(I) all: 0.097 / Χ2: 0.99 / Net I/σ(I): 6.9 / Num. measured all: 249117
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-1.9660.84220020.740.3720.9220.949100
1.96-26.10.76819890.7510.3360.840.93699.8
2-2.046.30.6319750.8290.2720.6880.99299.9
2.04-2.086.20.58219870.8330.2520.6350.98299.9
2.08-2.126.20.46219940.8960.20.5050.98999.9
2.12-2.176.20.41719960.9020.180.4551.00199.9
2.17-2.236.20.33119850.9410.1430.3620.997100
2.23-2.296.20.29819660.9520.1290.3261.015100
2.29-2.366.10.2620410.9620.1140.2851.008100
2.36-2.4360.21919730.9710.0970.240.99999.8
2.43-2.525.80.18819780.9790.0850.2071.00499.7
2.52-2.625.10.14820330.9830.0720.1660.99299.9
2.62-2.7460.13320090.9890.0590.1450.954100
2.74-2.886.70.11320000.9930.0470.1221.01100
2.88-3.066.70.09120370.9960.0380.0980.967100
3.06-3.36.60.06820370.9970.0290.0740.994100
3.3-3.636.60.05120200.9980.0210.0550.993100
3.63-4.166.30.03820760.9990.0160.0421.003100
4.16-5.245.50.0320680.9990.0140.0340.99799.9
5.24-506.30.03122200.9990.0130.0341.00799.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3dqz


Resolution: 1.93→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.959 / SU B: 6.412 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.13
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1901 2006 5 %RANDOM
Rwork0.1383 ---
obs0.1409 38317 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.47 Å2 / Biso mean: 30.417 Å2 / Biso min: 13.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0 Å2-0 Å2
2---0.04 Å20 Å2
3---0.56 Å2
Refinement stepCycle: final / Resolution: 1.93→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 68 343 4535
Biso mean--64.13 40.93 -
Num. residues----519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0194419
X-RAY DIFFRACTIONr_bond_other_d0.0020.024213
X-RAY DIFFRACTIONr_angle_refined_deg2.361.9745971
X-RAY DIFFRACTIONr_angle_other_deg1.18439744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6935545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92824.074189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91815788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0871520
X-RAY DIFFRACTIONr_chiral_restr0.1480.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214965
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021025
LS refinement shellResolution: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 132 -
Rwork0.226 2774 -
all-2906 -
obs--98.81 %
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)
10.61170.02650.03530.26820.20850.4172-0.01180.0840.0583-0.0351-0.0160.0034-0.011-0.02790.02790.015-0.004-0.00080.01920.00460.0094-8.1272-2.56373.3448
20.85480.06620.23540.5002-0.05220.07490.0121-0.1203-0.01520.0205-0.0158-0.0550.0012-0.03310.00370.007-0.0049-0.00670.0266-0.00650.02529.471-7.511132.9928
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 260
2X-RAY DIFFRACTION2B1 - 259

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