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- PDB-6cod: AtHNL enantioselectivity mutant At-A9-H7 Apo Y13C,Y121L,P126F,L12... -

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Basic information

Entry
Database: PDB / ID: 6cod
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 / Resolution: 1.8 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)59,4218
Polymers58,9542
Non-polymers4676
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-46 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.772, 87.002, 122.775
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,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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C7H6O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: 0.1 M bis-tris, 16% 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: 1.8→50 Å / Num. obs: 49649 / % possible obs: 98.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.034 / Rrim(I) all: 0.08 / Χ2: 0.907 / Net I/σ(I): 8.8 / Num. measured all: 252922
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.833.10.46622110.7880.2870.5510.73288.5
1.83-1.863.30.42723420.8460.2520.4990.74794.6
1.86-1.93.70.38323940.8740.2170.4430.75697
1.9-1.9440.35724300.8970.1940.4080.78198.1
1.94-1.984.30.3324910.9150.1740.3750.81399.2
1.98-2.034.70.324300.9420.150.3360.83799.5
2.03-2.0850.26224910.9530.130.2940.85499.8
2.08-2.135.10.22824630.9610.1120.2550.93999.7
2.13-2.250.19124790.9710.0950.2140.93699.8
2.2-2.274.60.15424830.9790.0780.1730.98599.5
2.27-2.355.60.14525000.9840.0670.160.99299.9
2.35-2.445.70.12324900.9890.0560.1350.99100
2.44-2.555.70.10824920.9910.050.1190.98399.9
2.55-2.695.70.09125080.9930.0420.1011.002100
2.69-2.865.70.07725100.9940.0350.0851.00299.8
2.86-3.085.60.06925320.9940.0330.0770.9799.8
3.08-3.395.50.05725250.9960.0270.0630.89599.9
3.39-3.886.70.0525650.9970.0210.0540.91599.9
3.88-4.886.40.04225820.9980.0180.0460.86999.8
4.88-505.70.04227310.9980.0190.0460.82299.7

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Processing

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

3dqz


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.936 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.11
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1938 2454 4.9 %RANDOM
Rwork0.15 ---
obs0.1522 47127 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.83 Å2 / Biso mean: 25.779 Å2 / Biso min: 10.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å2-0 Å2
2---0.43 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4122 0 30 286 4438
Biso mean--38.71 31.97 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0194300
X-RAY DIFFRACTIONr_bond_other_d0.0020.024088
X-RAY DIFFRACTIONr_angle_refined_deg2.5391.9635808
X-RAY DIFFRACTIONr_angle_other_deg1.23739457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3235526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4624.286189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06115763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1941517
X-RAY DIFFRACTIONr_chiral_restr0.1580.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214794
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02977
LS refinement shellResolution: 1.798→1.845 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 153 -
Rwork0.262 2968 -
all-3121 -
obs--84.58 %
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)
10.95430.0544-0.0090.43760.12960.5925-0.0340.16220.1-0.05430.00110.0171-0.0461-0.06070.03290.010.0026-0.00590.05730.01780.0132-7.9239-2.61593.4306
21.04260.10750.24580.48140.0060.2550.0056-0.16290.00360.0371-0.0053-0.02960.0027-0.0055-0.00030.0052-0.0026-0.00480.0563-0.01340.0169.4991-7.643133.2438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 259
2X-RAY DIFFRACTION2B1 - 259

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