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

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Basic information

Entry
Database: PDB / ID: 6coh
TitleAtHNL enantioselectivity mutant At-A9-H7 Apo, Y13C,Y121L,P126F,L128W,C131T,A209I with benzaldehyde, MANDELIC ACID NITRILE
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 / (2R)-hydroxy(phenyl)ethanenitrile / Alpha-hydroxynitrile lyase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.367 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)59,4196
Polymers58,9542
Non-polymers4654
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-19 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.277, 87.463, 123.990
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: 29476.996 Da / Num. of mol.: 2 / Fragment: AtHNL / Mutation: Y13C,Y121L,P126F,L128W,C131T,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-MXN / (2R)-hydroxy(phenyl)ethanenitrile / (R)-mandelonitrile


Mass: 133.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-HBX / benzaldehyde


Mass: 106.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.32 Å3/Da / Density % sol: 47.01 % / Mosaicity: 0.499 ° / Mosaicity esd: 0.011 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 0.1 M bis-tris, 20% 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: Nov 26, 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: 2.367→50 Å / Num. obs: 22909 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.066 / Rrim(I) all: 0.163 / Χ2: 0.612 / Net I/σ(I): 3.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.367-2.46.30.67911290.7850.2880.7390.44100
2.4-2.446.40.62511120.8150.2660.680.436100
2.44-2.496.30.55711200.8730.2370.6070.448100
2.49-2.546.20.49811140.8730.2130.5430.445100
2.54-2.66.10.45611370.8810.1980.4980.481100
2.6-2.666.10.40511450.9060.1770.4430.50699.6
2.66-2.7260.42411030.8930.1870.4640.65399.8
2.72-2.85.40.30611450.9260.1420.3390.53499.8
2.8-2.886.10.29711310.9430.1290.3240.551100
2.88-2.976.30.27911160.9320.120.3040.585100
2.97-3.086.30.2311320.9650.0990.2510.65499.9
3.08-3.26.30.19311280.9770.0830.2110.697100
3.2-3.356.20.16911730.9820.0730.1850.7499.9
3.35-3.5360.16411150.9790.0730.180.82299.6
3.53-3.755.50.13811540.9810.0630.1520.85699.9
3.75-4.036.40.1311530.9820.0560.1420.71100
4.03-4.446.20.10311700.9880.0450.1130.783100
4.44-5.0860.0911660.9930.040.0990.81699.9
5.08-6.45.70.08511900.9870.0390.0940.65799.8
6.4-505.50.07812760.990.0360.0870.45499.6

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Processing

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

3dqz


Resolution: 2.367→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.939 / SU B: 15.771 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.228
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 1178 5.2 %RANDOM
Rwork0.1516 ---
obs0.1547 21683 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 119.82 Å2 / Biso mean: 40.145 Å2 / Biso min: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 2.367→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4122 0 34 159 4315
Biso mean--49.75 39.13 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194289
X-RAY DIFFRACTIONr_bond_other_d0.0020.024077
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.9655792
X-RAY DIFFRACTIONr_angle_other_deg1.08339433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9825524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6224.316190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14515761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5261517
X-RAY DIFFRACTIONr_chiral_restr0.1110.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214759
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02975
LS refinement shellResolution: 2.367→2.429 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 73 -
Rwork0.213 1486 -
all-1559 -
obs--92.91 %
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)
11.63170.040.01660.7664-0.13561.0665-0.03080.2224-0.1214-0.1164-0.023-0.03190.09580.05620.05380.06360.00310.00750.0402-0.01610.01418.048990.0349127.46
21.90280.0124-0.19820.71340.05380.65620.0081-0.2474-0.00780.0924-0.01570.03330.0026-0.00520.00760.0522-0.00070.01220.04790.00940.0088-9.610495.2603157.5678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 259
2X-RAY DIFFRACTION2B1 - 259

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