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- PDB-8sni: Hydroxynitrile Lyase from Hevea brasiliensis with Forty Mutations -

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Basic information

Entry
Database: PDB / ID: 8sni
TitleHydroxynitrile Lyase from Hevea brasiliensis with Forty Mutations
Components(S)-hydroxynitrile lyase
KeywordsLYASE / Engineered Protein / alpha/beta hydrolase fold / esterase / catalytic promiscuity
Function / homology
Function and homology information


(S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity / jasmonic acid metabolic process / methyl salicylate esterase activity / methyl indole-3-acetate esterase activity / methyl jasmonate esterase activity / salicylic acid metabolic process
Similarity search - Function
Methylesterase/Alpha-hydroxynitrile lyase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
PROLINE / (S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWalsh, M.E. / Greenberg, L.R. / Kazlauskas, R.J. / Pierce, C.T. / Aihara, H. / Evans, R.L. / Shi, K. / Tan, P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119483 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIGMS R35-GM118047 United States
National Science Foundation (NSF, United States)2039039 United States
CitationJournal: To Be Published
Title: Hydroxynitrile Lyase from Hevea brasiliensis with Forty Mutations
Authors: Walsh, M.E. / Greenberg, L.R.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 2.0Feb 19, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / chem_comp / chem_comp_atom / chem_comp_bond / citation / entity / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_asym / struct_conf
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.title / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_ligand_of_interest / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length
Description: Model completeness / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (S)-hydroxynitrile lyase
B: (S)-hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1688
Polymers65,5872
Non-polymers5816
Water1,22568
1
A: (S)-hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1635
Polymers32,7941
Non-polymers3694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: (S)-hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0053
Polymers32,7941
Non-polymers2112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.527, 81.884, 90.929
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein (S)-hydroxynitrile lyase / (S)-acetone-cyanohydrin lyase / Oxynitrilase


Mass: 32793.594 Da / Num. of mol.: 2
Mutation: I9V, T11G, I12A, I18S, E79H, C81L, L84M, H103L, N104A, S105A, V106F, V118L, L121Y, M122N, F125T, D127N, K129L, Y133F, L146M, K147F, L148F, F150P, T151K, L152F, R154A, E155H, N156K, T159Q, ...Mutation: I9V, T11G, I12A, I18S, E79H, C81L, L84M, H103L, N104A, S105A, V106F, V118L, L121Y, M122N, F125T, D127N, K129L, Y133F, L146M, K147F, L148F, F150P, T151K, L152F, R154A, E155H, N156K, T159Q, T173V, G176S, Q180M, Q208K, I209G, F210I, L211P, K236M, L237A, Q238M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Gene: HNL / Production host: Escherichia coli (E. coli) / References: UniProt: P52704, (S)-hydroxynitrile lyase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.5, 0.2 M L-Proline, 10 % w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→60.85 Å / Num. obs: 39196 / % possible obs: 98.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 36.55 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.054 / Rrim(I) all: 0.086 / Rsym value: 0.066 / Net I/σ(I): 10.5
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2786 / CC1/2: 0.698 / Rpim(I) all: 0.774 / Rrim(I) all: 1.244 / Rsym value: 0.967 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→60.85 Å / SU ML: 0.2626 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7824
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2273 2007 5.13 %
Rwork0.1987 37109 -
obs0.2002 39116 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.36 Å2
Refinement stepCycle: LAST / Resolution: 1.99→60.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3995 0 35 68 4098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784144
X-RAY DIFFRACTIONf_angle_d0.93355636
X-RAY DIFFRACTIONf_chiral_restr0.0545610
X-RAY DIFFRACTIONf_plane_restr0.0071715
X-RAY DIFFRACTIONf_dihedral_angle_d6.8018547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.36111450.31642660X-RAY DIFFRACTION99.29
2.04-2.090.33691500.2932613X-RAY DIFFRACTION99.21
2.09-2.160.30241340.27092666X-RAY DIFFRACTION98.87
2.16-2.230.30981410.24342597X-RAY DIFFRACTION97.86
2.23-2.310.27411400.23982608X-RAY DIFFRACTION97.65
2.31-2.40.2621470.22572670X-RAY DIFFRACTION99.61
2.4-2.510.2781290.22022666X-RAY DIFFRACTION99.64
2.51-2.640.29251600.21972673X-RAY DIFFRACTION99.58
2.64-2.80.29891350.23122661X-RAY DIFFRACTION99.18
2.8-3.020.26191490.23312670X-RAY DIFFRACTION98.29
3.02-3.330.23731450.21642618X-RAY DIFFRACTION96.88
3.33-3.810.22691470.19472667X-RAY DIFFRACTION97.91
3.81-4.80.15781420.14842676X-RAY DIFFRACTION96.87
4.8-60.850.17471430.15922664X-RAY DIFFRACTION92.37

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