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- PDB-5tdx: Resurrected Ancestral Hydroxynitrile Lyase from Flowering Plants -

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Basic information

Entry
Database: PDB / ID: 5tdx
TitleResurrected Ancestral Hydroxynitrile Lyase from Flowering Plants
ComponentsAncestral Hydroxynitrile Lyase 1
KeywordsLYASE / HNL Ancestral Hydroxynitrile lyase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsJones, B.J. / Evans, R. / Wilmot, C.M. / Kazlauskas, R.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM102205 United States
CitationJournal: Plos One / Year: 2020
Title: Larger active site in an ancestral hydroxynitrile lyase increases catalytically promiscuous esterase activity.
Authors: Jones, B.J. / Evans 3rd, R.L. / Mylrea, N.J. / Chaudhury, D. / Luo, C. / Guan, B. / Pierce, C.T. / Gordon, W.R. / Wilmot, C.M. / Kazlauskas, R.J.
History
DepositionSep 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Oct 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: Ancestral Hydroxynitrile Lyase 1
B: Ancestral Hydroxynitrile Lyase 1
C: Ancestral Hydroxynitrile Lyase 1
D: Ancestral Hydroxynitrile Lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,02910
Polymers124,4774
Non-polymers5536
Water3,459192
1
A: Ancestral Hydroxynitrile Lyase 1
B: Ancestral Hydroxynitrile Lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5155
Polymers62,2382
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-18 kcal/mol
Surface area20140 Å2
MethodPISA
2
C: Ancestral Hydroxynitrile Lyase 1
D: Ancestral Hydroxynitrile Lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5155
Polymers62,2382
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-19 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.265, 108.265, 201.188
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Ancestral Hydroxynitrile Lyase 1


Mass: 31119.217 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: (S)-hydroxynitrile lyase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.44 Å3/Da / Density % sol: 49.66 % / Description: Octohedral, 220 um point to point
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1:1 mix of protein (in 5mM BES buffer) with mother liquor (1.1 Molar Ammonium Citrate, 50 mM bis-tris propane, pH 6.8) Crystals formed after 2-3 weeks at 20 degrees C. Crystals were cryo- ...Details: 1:1 mix of protein (in 5mM BES buffer) with mother liquor (1.1 Molar Ammonium Citrate, 50 mM bis-tris propane, pH 6.8) Crystals formed after 2-3 weeks at 20 degrees C. Crystals were cryo-protected in 5% glycerol in mother liquor for 10 seconds then flash frozen in LN2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 30, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.96→29.32 Å / Num. obs: 86348 / % possible obs: 99.3 % / Redundancy: 8.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.8
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.68 / CC1/2: 0.772 / % possible all: 88.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.42 Å29.32 Å
Translation2.42 Å29.32 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.1phasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YB6
Resolution: 1.96→29.32 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.339 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.148 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 4319 5 %RANDOM
Rwork0.1767 ---
obs0.1792 81902 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.94 Å2 / Biso mean: 38.133 Å2 / Biso min: 15.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.96→29.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8396 0 36 192 8624
Biso mean--54.09 33.12 -
Num. residues----1044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0198775
X-RAY DIFFRACTIONr_bond_other_d0.0020.028226
X-RAY DIFFRACTIONr_angle_refined_deg2.3461.96111924
X-RAY DIFFRACTIONr_angle_other_deg1.207319050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53951072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.48325.181415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.665151512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1611526
X-RAY DIFFRACTIONr_chiral_restr0.1650.21301
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0219887
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021963
X-RAY DIFFRACTIONr_mcbond_it1.9912.4984234
X-RAY DIFFRACTIONr_mcbond_other1.9912.4984233
X-RAY DIFFRACTIONr_mcangle_it2.7893.7295306
LS refinement shellResolution: 1.956→2.007 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 277 -
Rwork0.253 5496 -
all-5773 -
obs--91.46 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9679-0.5459-0.24651.07540.26491.1769-0.1002-0.0970.03960.13050.05130.04210.05850.12380.04890.07360.0513-0.00220.0471-0.00360.0097121.634583.57220.7366
20.6682-0.01170.09890.3592-0.05030.9359-0.08950.0170.07770.00390.03450.051-0.0417-0.04820.0550.04040.015-0.0210.04080.01860.0372111.101786.5046-12.67
30.73560.01390.02890.7736-0.12730.80630.03670.1149-0.0639-0.0115-0.01950.01430.18220.1859-0.01720.10120.0949-0.00410.0987-0.01140.0061139.044857.3076-7.8936
41.1433-0.760.43091.727-0.41171.5623-0.15430.11970.36180.2611-0.0641-0.4947-0.32480.5030.21840.0923-0.1022-0.10290.22890.07350.1925153.362789.5048-4.9648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 261
2X-RAY DIFFRACTION2B2 - 260
3X-RAY DIFFRACTION3C2 - 266
4X-RAY DIFFRACTION4D2 - 261

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